Given the Church's history of manipulating politics, choosing and overthrowing kings, burning "heretics" at the stake, and attempting to dictate the very nature of the universe, it would make sense, at face value, that an anarchist would reject the Church as just another state. I have a few blog posts waiting in the wings that address these issues but, for now, I will call upon the work of others to begin the discussion.
What's important is holding the Church to the moral standard set out by it's philosophy. Where I can reject the government of Empire (the USA) based on the philosophy enumerated and expressed in the Constitution and the actions of the "Founding Fathers", that same opportunity is drastically diminished, if not impossible, with regards to the Church.
This article begins to explore this reality.