I think everyone is forgetting that when the decision to make Sim was made, Phlox thought he could harvest the parts needed without killing Sim. So they would have Trip and a copy of Trip with a short life span running around. After Sim grew up Phlox realized the procedure would kill Sim. I don't think the decision to make Sim was morally wrong, it's no different than parents who have another child to use the stem cells from the placenta to cure an already sick child they have. What unfortunately happened was that it turned out the surgery would kill Sim. That's when the dilemma came in. Well, and the dilemma that Sim only had a 15 day life span, but whose to say that's better or worse than being a slug in a jar.
(Not going to even touch Tuvix.)