The episode says some incredibly frightening and bizarre things about Federation morality. To me, the issue comes down entirely to consent. Kurn gave his consent to be killed, he wanted to die, there were just strange cultural reasons he couldn't hold the knife himself, so he wanted his brother to do it. Kurn didn't give his consent WHATSOEVER to be mindwiped, brainwashed and surgically altered to completely gain a new identity. So to have the enlightened Federation yell at Worf for trying to do the first while having no problem and help him do the second is unusually barbaric. This isn't even "Ooh, DS9 is showing the Federation ain't all that, they're dark too..." It's like they don't even realize the horrific implications of their pulled-out-of-their-ass ending to their anti-euthanasia episode.