The Captain is a military official, not a "god". There are some rights that people take as basic. Rights upon which it is morally improper for human institutional figures to infringe.
If the Captain had decided to discriminate against or repress certain crewmembers on the basis of their religious beliefs, for example, I'm sure we would both agree that this falls outside of the scope of a captain's rights.
Here, B'Elanna has expressed her moral belief and asked that the Captain respect it. Surely, if the captain felt that B'Elanna was "wrong" in her judgment, she had every right to relieve B'Elanna of duty. But to force her to undergo a medical procedure?
It's akin to forcing a member of your crew to undergo an abortion, or ordering them not to. Not your place.