She should have simply teleported everyone on the ship into the Tuvix collective.

I think the reasoning is pretty solid, stemming from the many vs the one.

Keeping Tuvix saves 1 plant. Removing the plant and splitting Tuvok and Neelix back saves 2 lives.

2>1.

Is it still shitty? God damn right it is. But it's still logical, even if a bit sterile.