so....unless he's willing to kill, he should not be allowed the same freedoms as everyone else?

um....ok. Let's give him a job at an abortion clinic with your blessing. (/joke)

the fact is, many people have radical changes of heart. The army has in place procedures for such things.

Not great procedures, but procedures.

I'm really confused though why pacifism is not understood by a religious man?

I think the earlier suggested compromise was a good one: make him serve in some capacity that does not require him to kill anyone. Contracturally he complies, and ethically he retains his ideals.