I think the controversy of Janeway’s choice is largely due to the show’s failure to address the orchid of it all.
As I see it, Tuvix is not “Tuvok + Neelix,” but also isn’t “something new.” I maintain that Tuvix is primarily the orchid, which has subsumed the essence and personalities of two Voyager crew members and is asserting itself on board the ship.
All it would have taken is for Janeway to have maintained (or be convinced by another) that this was the case, and it would be the obvious choice to split them back up.
Of course that would negate the tension of the episode, but it could be left as “not everyone on board agrees that this is who/what Tuvix is, but Janeway believes it so that’s why her decision isn’t immoral.” We could have the same kinds of “was Janeway wrong?” debates, but some of the rough edges would be smoothed out, I think.