Religion, and here we are talking the Catholic faith, begins with an assumption: The universe is bigger than our ability to perceive it. Putting it simply, atheists and Catholics make opposite assumptions about the same thing. To whit: "Is there more to the universe than what we can perceive either aided or unaided?" Atheists assume no. Catholics assume yes. That is always the starting point.
Atheists live by reason, many non-Catholic Christians live by faith and Catholics live by faith and reason.
When one says that religion is the enemy of society and critical thought, he or she comes from an assumption that those who enact reason have a full understanding of the universe. They believe that the universe can be strictly and exhaustively defined in the material world by the physical properties of matter and energy. When we say that we adhere to our Catholic faith then we understand that means everything in terms of the reality of the material world but that there is also a deeper reality than we can perceive, in the spiritual world. To be fully wise, one needs to take into account the perceivable and the non-perceivable reality which means that which is material and that which is spiritual. How we understand both the material and the spiritual will be reflected in how we live our life.
So without question, religion would be the enemy of society and critical thought if indeed there was only the material world. However, if there is also a spiritual world, those who think strictly within the material will not be able to address existence fully. They will not be able to answer all the questions needed to create a just society and their reasoning will always fail to complete the task of a just society for all people.
In Catholicism, we understand all of that and realize since the universe is bigger than our ability to perceive it, we need to take that into account when we define ourselves and how we live our lives. We do that by listening and following the one who teaches of that reality and is leading us to the fullness of existence in both the material and spiritual worlds: That is Jesus Christ.