I'd say there's a difference. Tuvix wasn't some random crewmember; he only existed because of the loss of Tuvok and Neelix, because he's using their bodies/molecules/lives to exist. So I can see the argument that once Tuvok and Neelix can be restored, they are entitled to get their bodies/molecules/lives back, and Tuvix is not entitled to keep the bodies/molecules/lives of those two innocent people, even to preserve his own life.
That argument might hold water if Tuvix had been a malevolent parasitic alien who forcefully and intentionally stole their bodies. But that's not what Tuvix was. He didn't choose
to take their bodies or to be created. The very fact that he was alive meant he had a right to be. Killing him to restore Tuvok and Neelix was in effect punishing
him for the crime of...wait for it...existing.
"Dear Doctor" is ridiculous and stupid. I can't even go there.
"For The Uniform" is a strange one. Personally, I choose to think Sisko intentionally created a situation where the human and Cardassian colonies had to trade places which is somehow better for everybody. But that's just the head-canon I came up with in an attempt to justify the weirdness of Sisko's actions.
I liked Dear Doctor...because I don't mind the controversy.
The problem isn't controversy, the problem is that the view presented in the episode as praiseworthy are just plain wrong.
"In The Pale Moonlight" is a bit different. "Dear Doctor" presents an ethically wrong and morally disturbing attitude as the objective truth and then pats itself on the back. ITPM doesn't do that.