Just because he was brought into being in a manner that's different from us doesn't invalidate his life or give him any less rights than anyone else. Frankly that's a bit disturbing that you so casually remark that just because someone's different they're less of a person. But it's a common theme in humanity to dehumanize anyone to rationalize their death in their mind.
My position has always been that Janeway has an obligation to the lives of her crew, and to do what's best for the ship. It's not a question of whether it's "right" based on human rights moralities, but whether it's to the benefit of the ship.
Disclosure: I have never been a parent, so this undoubtedly affects how I view the issue.