It is not so much Hook should have put his foot down, so much as he should have tried not to profit from betraying Bae. Keeping Bae safe for his own good may have been as Snow calls it “the hard path”, but it seemed Hook had already set him up, rather than warning Bae. He may have been willing to cancel the betrayal, if Bae didn’t reject him for suspecting exactly that sort of thing in the first place.
^ This is why I think Neal will be far less tolerant with Hook than Rumple. Hook brought just as much pain to him as Rumple did, but Rumple at least would’ve never betray him out to the enemy like Hook did. Having experienced that, does anyone really think he’d trust Hook with Henry’s safety? For all he knows Hook’d do that just so he can extort Peter Pan of something.