Can an atheist be a conscientious objector?

Yes. The American Humanist Association resolved the religious bias in Conscientious Objection (CO) law way back in 1965 in US vs Seeger. (Also see Welsh vs US, 1970.) While CO status is assumed to be reserved only to the religious, atheists and humanists with strong moral objections to war may be exempted. That having been said, remember this must be objection to war in general not to one war in particular. There is no standing whatsoever to disagree with a certain specific war or military action. The two categories are objection to any involvement with military action at all. In this case, the person will be excused from service. The second is objection to personal violent action. In such a case, the person would be given an administrative position rather than a war-fighting position. In both cases, the paperwork and justifications will be extensive, but for those with strong conviction, it is entirely possible. Also, anyone who joins the military has effectively stated that they do not have a conscientious objection to war. Therefore any later CO status application would have to include a clear explanation of what changed between enlistment and CO status. A religious conversion is an obvious excuse but a change in secular thinking may also be the case.