I think bringing up arguments like "it's a tv show" are dodging the issue; Janeway et al. don't know they're on a tv show.
I also think it's rather awful to bring up things like "Tuvix was creepy!" as an argument against letting him live, even jokingly. I don't believe humans have any place saying that one life is more or less valuable than another. That's the kind of argument Khan and his cronies would have used to purge the Earth of "inferior" humans so that they could have the planet to themselves...and they'd probably also argue that in the end they would benefit more (important) people than they were harming and that it was for "the greatest good".
These all seem to be aimed at my ponts so to counter; I think it's a bit pompous to ascribe lofty ideals to what is after all a bit of space-based storytelling centred around human dilemmas. Dodgy decisions by captains abound in ST (Captain Picard excepted). Aside from that, comparing doing away with one accidental construct to recover two other people to genocide is, well, a bit OTT?