They established very early this season, that Rumple could not kill Peter without killing himself. “If he dies, I die”. And Regina never questioned Rump,e when he said it, implying that she understood 100% what Rumple meant by that.
Honestly, when you look at this whole first half of the season, nothing adds up. Storybrooke is gone, oops, no it’s not. Emma will never remember, oops, yes she will. Rumple is dead, oops, no he’s not. Next time I see Bae I will be putting his son in his arms, oops, no you didn’t. Regina, 100% redeemed! I doubt it. There is no cure for dreamshade, uh, yeah there is. You can never leave Neverland, oops, you can, if you have a coconut. Peter Pan never fails…..oops? (He better be dead.) Honestly there were more mistruths told about Neverland than I can remember.