Making Tuvix horrible by taking the worst aspects of Tuvok and Neelix could have been interesting, not to the point of being incompetent, but just horrible. Then we would probably have Janeway resist dividing him for some reason.
Seriously though, having the moral dilemma with an unlikable character could have been interesting. As has been pointed out, there is no moral standard for killing someone who is unlikable, but what if that is a nagging concern in everyone's mind. The key is, everyone is aware of that reason, and they actively resist its allure, because they know it is morally repugnant.
Instead Janeway leans on utilitarian reasoning for her decision to make the split. Yet, while everyone is celebrating Tuvok's return, maybe Neelix's too, Janeway is in a corner brooding. Chakotay approaches to ask what is wrong, and Janeway reveals her ambivalence over what was truly driving her decision. Did utilitarian concerns drive her decision to return Tuvok and Neelix, or did her dislike for Tuvix-git subconciously create her decision first, with the logic following later? Is either reason really better than than the other considering they both lead to the same conclusion? She is racked by doubt, but has enough presence of mind to know she will not change her orders even if she changes her mind. A captain must live by their decisions and be decisive.