Yes, the government used to evaluate the legitimacy of religious convictions when it decided whether to assign conscientious objector status. Lifelong members of religions with a long history of pacifism were almost automatically granted conscientious objector status, based on the legitimacy their religion built up over time. That legitimacy was built by the
actions of past members demonstrating the beliefs were sincere; not on the beliefs themselves.
That changed some in 1971, with the USSC's ruling in
Gillette v United States. Conscientious objector status should be based on the individual's beliefs about war, not what religion he belongs to. Except when a person is only 19, it's a lot harder to demonstrate a personal history of being opposed to war than it is to show membership in a church, so some bias, whether intended or not, is practically unavoidable.
In other words, it was a legitimate concern for the military that many draftees with no prior opinions about war would suddenly find the idea of personally dying in a war to be very objectionable. The military was justified in asking for some objective confirmation that a person was, and had been for some time, opposed to war on moral grounds (and not political grounds).
Gillette v United States is also why Watada had no chance to win his case about deploying to Iraq, since it upheld the government's stance that a person couldn't be a conscientious objector to one particular war. Objecting to a particular war would be objecting on political grounds; not moral convictions about war in general.