Autumn is actually the only Enclave character in 2277 that really believes in Enclave's holy mission. He does, afterall, constantly refer to the country as United States and talks about the line of presidency, while Eden mentions the United States only once in the radio. And while he talks to you at the purifier, knowing that he has nothing to lose, he does seem like telling what he's really thinking. He wouldn't be the first Enclave person to strongly believe in Enclave's good side. His methods just svck and make him look like a total bad guy.
Richardson's Enclave was just as bad. Their philosophy is exactly what Eden's is.
Also, Autumn still shoots innocents and still considers anyone who is "impure", dirt. He would never treat a wastelander as his equal, not even close. Eden's Enclave and Richardson's Enclave ARE the Enclave. Autumn doesn't lead the Enclave. He is one person with perhaps only a few soldiers following him. We know that Autumn doesn't like the FEV idea, but only Autumn. Both known leaders of the Enclave supported use of the modified FEV and so most of the Enclave would have as well. The true Enclave has made that their goal. Fallout 2's Enclave was attempting the exact, same thing. Autumn is still part of the Enclave and still follows their philosophy, but only he has been confirmed of disagreeing with this one thing, and of course there will be some who disagree, but Autumn and a couple of his soldiers do not represent the Enclave. He didn't even appear in Fallout 2. Face it, the actual Enclave supports the eradication of the "impure".