If an atheist had said that Muslims attacked America because we are an atheist nation, would a violation have occured? Or is this one of those Christian-only rules?
If he had done so wearing the uniform of the United States Army, without issuing "a required disclaimer at the speeches that he was not representing official Pentagon policy," and forgetting his "oblig(ation) to clear the speeches," then yes a violation would have occured.
I don't see anything here to indicate that it's a Christian-only rule or that he's being singled out for his views. Quite the contrary, the report quotes his "outstanding record" and refuses to reprimand him. But the DOD wants to have some measure of control over what you say publicly while in uniform. Especially a general.
If you have information that similar remarks from atheist, Jewish or Islamic generals were ignored, then I'd like to know. Until then, this action seems proper to me.