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Sorry if someone already proposed this.

What if Tuvix was a unstable merging. That the Doctor found out that eventually he would experience cellular breakdown after a certain amount of time. The episode starts off fine with Janeway OK with Tuvix. His cellular breakdown happens, the Doctor is trying to find a cure. But he figures out two possibilities. One that can correct it but has let's say a 50/50 chance but he like the original can seperate Tuvix back into Tuvok and Neelix but has let's say a 80% chance of succeeding.

Tuvix wants the 50/50 but Janeway wants to try to seperate him back. There is scenes with Janeway recognizing Tuvix as a new being and is reluctantly accepting that Tuvok and Neelix is gone and doesn't want to kill Tuvix to try to get the original two back.

But at the same time, she has to decide on based on odds of success.

I think that would have been a better option.

I can't even begin to figure out how I would talk about Tuvix. Like, I believe Janeway murdered Tuvix, but Tuvix should have never existed. This Tuvix is an incredible idea for science fiction that could be made into a miniseries. "I forgive you."

Edit: In a search for the Tuvix moral quandary, I've come across this review of Tuvix.