^You know, that's a fair point. I hadn't thought of it that way. I don't buy the argument that they should've let Tuvix stay because the other two were already dead, but there is something to be said for the argument that if they'd let him stay, nobody would've died. Although one could argue that neither of them consented to the joining, so there's still an ethical question about forcing them to remain joined forever. Like I said, not a simple issue.
It was the quintessential no win scenario I think no one would want to face. After watching the episode, you could see Janeway struggle with the decision she was forced with. The final straw was Kes breaking down in her ready-room, it would seem her maternal instincts kicked in and she decided to restore Tuvok and Neelix. Not only did she decide Tuvix's fate, but she spared anyone else of having to carry out the execution. I would definitely love to see this guilt creep into Janeway in a future novel...especially now that she is in a more emotionally compromised state after all she's discovered.
Now, the writers could have come up with some techno-solution to keep all three of them alive, but that would have cheapened the episode; Data saving his love and her father would have done the same thing.