Janeway had a responsibility to restore her crew to their original status. Both Tuvok and Neelix were unharmed while integrated as Tuvix, therefore Tuvix remains unharmed while split back into the original individuals. If Tuvok and Neelix wished to recombine, they could both consent and do so.
I think because that involved a planet and a semi reflective atmosphere, it would be difficult for voyager to reproduce.
Although you'd think cloning would be relatively easy with the transporter and replicator technology, but there's probably some canon reason it's not.
I doubt replicated fruit has viable seeds. I suspect Gene Roddenberry wanted to reserve room in the universe for the idea of the soul, and the unknowable mysteries of metaphysics.
I don't cheer for it but at the end of the day, I agree with Janeway's decision. And if eating plants isn't murder, killing Tuvix isn't either, since he was the result of an alien plant messing with Neelix and Tuvok's DNA while in the transporter. If anything, she merely did a little weeding in the garden that is her crew.