He probably did dislike the 'thou shalt not's, but his main gripe was what he called "slave morality" - which is pretty much the opposite of stoicism. An important distinction is that he didn't disagree with Christ - he disagreed with the church. IMO, he understood Christ better than anyone in any physical church. Something I'm seeing is that the church tends to eject anyone who actually understands - and the more constipated the church, for example Catholic or EO, the less tolerant they are of real followers of Christ.
Discussion
I agree that his critique of the church is incomplete. We've had another 100 years of the great conversation he didn't have when we point those missing things out. Standing on the shoulders of giants.
As an atheist, I'm currently most interested in the way christians and the church use god and the devil to absolve themselves of personal responsibility. The devil made me do it may be said in jest, but it is a real view that taints how they act in the world. Outside forces beyond their control can force them to act in ways they would not choose to. It is like living with the ultimate case of learned helplessness as your core belief of how the world works.
Interesting perspective. I've fairly recently become a Christian, after being agnostic but spiritually curious for a long time. So far, almost universally, the Christians I've met have been all about taking responsibility. Sometimes annoyingly so... This is also pretty close to that crack in the matrix I mentioned.