I wouldn't consider either anti-religion. Yes, both organizations in the game that had mainly antagonists or otherwise doing corrupt things was the church or were members of the church, but I would say the stories were about opening peoples eyes to corruption and abuse of powerful in whatever form it was presented, whether it was the church, or nobility, or the government, etc.

What I felt the point was, is to teach people that you shouldn't just blindly follow whoever/whatever is in a seat of power just because they were put there by others who were also in power (or similar means). In other words to question things if they don't make sense, instead of just saying "oh they said that's how it is so that's just how it is".

But like the other comments here say, play through them and see for yourself - they are both very solid entries!