Given that part of the point of the Strike in the first place was to
prove that looter governments would eventually collapse when they were
deprived of people to enable them, was the fact that Francisco
d'Anconia (and, for that fact, Ragnar Danneskjöld) was deliberately
destroying the economy contrary to that goal?
There are two answers to that question: yes and no. Which answer you accept depends whether you accept either of two connected premises Ayn Rand 'pushed' in the book. If you don't accept them, then the answer is "Yes, and they are very hypocritical about it". If you accept one of them, the answer is "No, it makes perfect sense, they were just trying to save the thousands of innocent people by hastening the collapse."
The first idea can be summed as "If there is not the best person for the job doing it (or at least the person in top ten), the job wouldn't get done at all and the whole system will grind to a halt. And everybody knows who the best person for the job is." and that's the whole idea behind The Strike. The thing to know entertaining the idea here is that Rand never worked in a business or a corporation. She never did any scientific research either. As a rule (with certain exceptions) writing is a solitary profession. Business and scientific research are not. Businesses and scientific research are built on the work and knowledge of many individuals.
I'll get back to this idea later. The idea leads to her second idea.
The second idea is so called "impotence of evil" . Basically, the idea that evil people can create anything useful and prosper in the long term without the good guys helping them was absolutely unbelievable to Rand. It is shown in the book itself with Galt fixing the machine used to torture him. The idea is basically "the only thing evil needs to win is for the good men to do nothing to prevent it" with addition of "or to keep doing their jobs for the wrong reasons". Because evil can't create, it cannot even maintain what greater ("good") people created, not even to further its goals. It can only destroy.
Short answer: the heroes believe and the narrative that is pushed is: the world is doomed anyway, everything is going downhill quickly and the heroes want to hasten that doom so they can start the rebuilding process sooner. Basically, let the system burn down completely before rebuilding it from the ashes. Make it from 0 instead of fixing the existing one. Which is example of broken window fallacy, because it is easier to peel a few spuds off the current system than destroy and rebuild. If that is the case, then the answer is "No, destroying shipments wasn't contrary to their goals". And why didn't they use them and repurposed them for something else? Because that would have made them moochers and looters. The more interesting example is Ellis Wyat burning his oil fields, which demonstrates lack of understanding of negative externalities and would be an example of ecological terrorism.
In real world, sometimes people are doing jobs they are not perfect for. In fact, they sometimes are assigned tasks they are ill suited for. And they do them anyway, to the standard lower than what an expert for the job would have done, sometimes much lower, but (and this is crucial) it still somehow works. There are three possibilities: either
option 1) the task is done perfectly or
option 2)it is done badly but it still works or
option 3)it is not done at all.
If it is
1) done perfectly, everything is good with the world. That is what Randian hero would do.
If it is
2) done badly (and badly here means anything less than perfect, from barely works to slightly worse than what the best of the best would have done. Basically everything which can be improved later if you tomorrow call an expert in), it is done in such a way that after the task is finished, it still works. Not as efficiently as it would work if it was expert doing it in the first place (in fact, if expert saw it they would say it was done by rank amateur and suggest improvements immediately), but it still works. It does its designed purpose. If it doesn't, you get straight to option 3.
Option 3: The task wasn't done. Our current workers and expertise tried their best, they really did, after trying for a month they decided the task and change behind it as designed and decided is impossible to implement. That means back to the drawing board, we will have to figure something else, some workaround to the original problem which is not the current solution/task which we found that it is impossible for us to implement.
Now, that's one of the reasons immigration of the best educated and most efficient workers from the economy is bad. Your expertise is going away and your growth slows down considerably. It slows down, but it never stops completely. Why not? Because expertise and knowledge can be gained and given time and resources even the lowest worker on the assembly line can become expert in something! Which was almost anathema for Rand.
She was in love with idea of natural born geniuses without understanding technological and societal basis for innovation. Or basis and origination of societal welfare and wealth. Thus the idea that somebody could do the job badly but not badly enough that it doesn't work out in the end is impossible in that book. And that's why The Strike works. Because in the book the job is either done by the best or is not done at all. Without a few thousand supermen in power things are not getting done and are collapsing. In real world, you would replace a single superman with 3, 4 or 10 regular people and keep on going. In time, one of them will become 50% superman, or 75% superman. They might never become a genius like the original, but they would be good enough for the system to keep functioning. And growing and innovating too.
In fact, there is a metric which measures whether the project will fail if one member of the organization or project team is taken out. It is called the bus factor and organizations take care to ensure continued existence if something happens to a key team member or leader (eg they get hit by a bus or join The Strike).
And because Rand didn't really understand economics and basis for wealth of society, she thought that it is better idea to burn everything to the ground and then rebuild than to just innovate and fix the problems with the existing world. The truth is, if there is big enough societal collapse, there is no quick rebuilding possible. And as Mike Rowe's "Dirtiest Jobs" show demonstrates, you need some really dirty jobs for our shiny civilization and technology to be possible. Like the picture below hints at with tongue firmly in cheek.
Edit to clarify after comments, because I focused on Dagnar and background more than on Francisco:
What Francisco did fits definition of industrial sabotage. And fraud. And wide definition of terrorism, e.g using fear and violence to make people change their habits and convert them to his way of thinking.
He used the weakness of quality control mechanisms (which were set up by Francisco himself) to intentionally do a subpar job which caused people to die. And he basically used the excuse every fraudster ever used to justify himself. "If they were smarter, if there was one good and smart guy among my victims, I wouldn't have been able to pull it off. They got exactly what they deserve." .
Again, keep in mind that Ayn never worked in business. And that she believed in those two things above. And that she decided to make the world and characters intentionally archetypal, sharper than they would be realistically, all to prove the point.
I'll again compare real world and the world of the book and this is going to be a long edit, so...
In real world, contractors are not just chosen according to their price and their needs. When the project is made and contractors chosen, minimal standards of quality are decided on before choosing the contractors to do the jobs. Even after choosing the contractor, there are minimal standards of quality that their work has to fulfill to be accepted and contractors paid. There are multiple control mechanisms which check for defects, workarounds and shoddy work. The contractor is forced to fix defects found before the work is accepted as good and the next phase of the project begins. Once the final phase of the project is complete, there is final sets of checks which says "Yes, this work is done and it can now be open to the public. " or "No, you need to fix these major problems before it can be allowed. These minor problems can stand."
There is penalty for every major defect found and for every day the project is late.
Now, we get back to her "impotence of evil" theory. In the book Francisco intentionally hired the worst contractor he could find. He intentionally crippled every quality control mechanism, by firing any competent person from the Quality control commission and by bullying any competent worker of contractor he hired to do subpar work. In his mind, Francisco is doing exactly what the looters are doing. In his mind, he is following the principles of the looters to the letter. "If there was one truly good and competent among them, that person would stand up to Francisco" Ayn says. The only way the evil can win is if the good people do nothing and let themselves be bullied - she says. Except, Francisco is one of Ayn's supermen. If there existed superman to oppose him, he would have instead joined him on moral principles else he wouldn't be superman!
Francisco is wrong. Ayn wants to have her cake and eat it too.
There is a difference between doing something bad unintentionally, from incompetence and doing something from pure malice. Ayn wanted to prove that planners are incompetent, even when they think they are acting rationally.
She chose to prove it by planting the saboteur at the highest level of the enterprise who doesn't act rationally. Unless you know he is saboteur and fraud, then his behavior makes perfect sense. Keep in mind, the victim of a fraud often finds out it was tricked only after the fact. Then all that weird behavior you dismissed earlier starts to make sense. Those were the warning signs you chose to ignore and have suffered for it.
So, genealogy of the fraud which potentially left thousands of people dead and hundreds of people ruined from the point of view of defrauded businessman:
Francisco, a man who up to that point always turned profit in all his business endeavors, starts gathering money to buy some mountains and build a settlement. He is in copper mining business, so you logically assume that he found some rich vein of copper there.
He always acted rationally before, he always worked with a profit motive and his self interest at heart, he is a trusted member of the community. Investing in him was always a sure bet (Rand emphasizes that point multiple times). Asked for a few investments, some people you trust invested in him. You ask for details. He provides them to you. You invest in him too.
He starts working on his project. A few months later, the project is a failure and it turns out Francisco sabotaged it. He ruined himself and the other people intentionally. A year before starting the project, he joined some "End of the world" cult and has decided to get rid of all his worldly possessions so he can join Heaven. Nobody knew about that before investing else they wouldn't have invested in him. When asked why did he do that, he replies "If you weren't so rotten and fallen, you would have been able to stop me. This proves that I am right and just, that I am one of the chosen ones. Heaven's gates are now wide open for me. And all of you got exactly what you deserved, sinners as you are, this is just punishment for your sins!"
"But thousands of innocent people have died! Miners and their families! Children died." You reply weakly.
"If they were smart people and true believers, they would have noticed all the shortcuts I have used, all the defects, all the shoddy workmanship. They were sinners, all of them, enablers! Each and every one! They got what they deserve!" Francisco replies, his eyes burning with the fire of fanaticism.
When put like that, it makes just as much sense as his explanation. And that's what the scam was, if you look away from the text a bit and assume that the two principles Ayn Rand pushed in the book do not quite hold up to scrutiny. And that heroes are not quite reliable. But that would be breaking the suspension of disbelief. You can read the quotes in the answer below.