But, Henry now thinks of Regina as Mom?
My EXACT biggest problem with the episode. He's never thought of her or treated her that way, much less referred to her that way.
I don't know why they went with that motivation instead of the obvious (and better) one: that Henry, like Emma, is the human moral compass for the fairytale characters.
It's not "don't kill her, she's my mom!"
It's: "don't kill her: YOU are not the bad guys, SHE is! And the good guys don't act like the bad guys!"
Moral compass, yes. "Don't kill my (never cared about her before) mom!" - no.
Otherwise, it just becomes a second emotional bribery echoing Rumpel/Belle - and doing the same thing twice takes away from the Rumpel/Belle promise too.