If you recall, when Janeway was debating the ethics of the situation, she said it would have been a completely different issue if the transporter accident had been reversed shortly after it happened. But a long time transpired, allowing the "accident" to have a personality and life of its own, as opposed to the combined Neelix and Tuvok simply waiting to be separated.
This was one of the best episodes of the series because of the ethics and morals being discussed, and perfectly cast with Tom Wright. If she did not restore Neelix and Tuvok, she would be killing them. If she did resotore them, she would be killing Tuvix. It's a case of damned if you do and damned if you don't. A decision had to be made. One could argue that Neelix and Tuvok actually had died because technically, they no longer existed, therefore she was bringing them back from the dead instead of accepting their deaths and accepting Tuvix as a new life. Then we veer from real-life debate to the decisions of writers of a fictional show who want the characters restored so it was obviously going to be how that episode was resolved. One could debate this endlessly.
If I'm reading you right, your question about the uniform was more why were the two officer's uniforms melded together when the transporter accident was a result of biological matter being affected by the properties of the plants Neelix was holding when he was being transported. Why would that have affected clothing? It shouldn't have. Just as in Terminator, they should have been naked. But again, we are dealing with writers who decided to have Tuvix wearing a combined uniform instead of no uniform.
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