Oh, this one's up there with Equinox as a can o' worms.
I think the viewer should walk away with mixed feelings after seeing this one. The writers (and actors, judging by Janeway's face in the final scene) wanted it to be that way.
However, I am a heartless and terrible person, and thus was generally fine with Janeway flipping the switch. I look at it this way: people like Chakotay could have lived with the change (by the by, his line to Janeway about Tuvix being a better creature than Tuvok when Tuvok is her oldest friend was a total dick thing to say. I'm shocked she didn't slap him. But I digress.) But people like Kes could not. If Tuvix stuck around, there would have been mountains upon mountains of resentment in the Kes camp. They would have been inwardly pissed at Tuvix and probably at Janeway for sitting on her hands.
Not to mention there was the whole selfish reason of Janeway wanting her friend back. She would have had to work every day with the guy and wonder "what if?" Kes, as well - and anyone else attached to either Tuvok or Neelix. The cat was out of the bag; the separation treatment was available. It would have hung like a specter over their heads the whole time.
Anyways, Tuvix himself helped develop his own treatment, and then suddenly backed off at the eleventh hour and got pissy. He didn't have an inkling during that whole time that the treatment would "kill" him? Why did he help?!
I dunno. YMMV, and with this episode, I'm sure it does.
