What makes Sammy think: "Poor kids, I began to feel sorry for them, they couldn't help it" has nothing to do with his own reaction.
It isn't only Sammy and McMahon that were entranced by the situation.
Everyone in the store was too, male or female:
The sheep [other customers] pushing their carts down the aisle […] were pretty hilarious.
You could see them, when Queenie's white shoulders dawned on them, kind of jerk, or hop, or hiccup, but their eyes snapped back to their own baskets and on they pushed.
I bet you could set off dynamite in an A&P and the people would by and large keep reaching and checking oatmeal off their lists and muttering "Let me see, there was a third thing, began with A, asparagus, no, ah, yes, applesauce!" or whatever it is they do mutter.
But there was no doubt, this jiggled them.
A few house-slaves in pin curlers even looked around after pushing their carts past to make sure what they had seen was correct.
You know, it's one thing to have a girl in a bathing suit down on the beach, where what with the glare nobody can look at each other much anyway, and another thing in the cool of the A&P, under the fluorescent lights, against all those stacked packages, with her feet paddling along naked over our checkerboard green-and-cream rubber-tile floor.
[…] our town is five miles from a beach, with a big summer colony out on the Point, but we're right in the middle of town, and the women generally put on a shirt or shorts or something before they get out of the car into the street.
And anyway these are usually women with six children and varicose veins mapping their legs and nobody, including them, could care less.
The girls are so out of place here that it's impossible for anyone not to notice and react.
In particular, the Manager finally notices them:
He comes over and says, "Girls, this isn't the beach."
"But this isn't the beach."
His repeating this struck me as funny, as if it had just occurred to him, and he had been thinking all these years the A&P was a great big dune and he was the head lifeguard. He didn't like my smiling — as I say he doesn't miss much — but he concentrates on giving the girls that sad Sunday-school-superintendent stare.
Queenie's blush is no sunburn now,
"That makes no difference," Lengel tells her, and I could see from the way his eyes went that he hadn't noticed she was wearing a two-piece before. "We want you decently dressed when you come in here."
"We are decent," Queenie says suddenly, her lower lip pushing, getting sore […]
Sammy feels sorry because of the "they couldn't help it" aspect, their being so clueless about the situation they had created.
That is why, despite their naïvely causing embarrassment to everyone in the store, he reacts when the Manager deliberately causes embarrassment to them.
Now here comes the sad part of the story, at least my family says it's sad but I don't think it's sad myself.