It is, certainly if you are told of it, inescapable to see the parallels between Moreau's converting beasts into men and England's "attempts" to civilize "colonials" (Did the spreaders of the British empire actually care about "civilizing" India? Forgive me for this -- I sure do not think India needed the British to civilize them and am reminded of what Disraeli said to an antagonist about his own ancestry when it was disparaged by a fellow MP.)
But is there any evidence at all that Wells set out to write a story about colonialism or even that he was subconsciously influenced to do so? I think anti-vivisection and animal rights were beginning to become important issues in an England which still had bear-baiting and ratting as blood sports. (And we had terrible things in the USA also.)
Is it not possible that Wells simply came up with a very creepy story idea and the animals were not stand-ins for Indians and other peoples? I note that some movie adaptations of The Island of Doctor Moreau seem to really hammer the theme -- if you did not know that the humans had been animals, you would indeed, based on appearance, names and manner of speech, simply think they belonged to a different ethnic group than the main human characters.