It's been a while since i've seen "Thine Own Self", but she had to order some to their death in order to save the ship. There was no pressing emergency that required Janeway to order to Tuvix's to his death. Furthermore whilst Tuvix was a combination of Tuvok and Neelix he never attended the Academy and so Janeway couldn't order him to his death. He was in essence a civillian, sure she could put him off the ship. As for needing a tactical officer Tuvix seemed fully capable of fufulling that role.
And whilst a Captain has a responsibility to the ship and her crew, she also has to uphold the ideals and principals of the Federation. Sometimes upholding those ideals and principals puts you in a negative position.
As for VOY number of crew, one episode it was 132 next it was 140, then it was 142. So they seemed able to make crew appear out of thin air.