This reflects my experience as well, @tryskele, and it is why I left the church. I won't tell my own story here, but it was very difficult as my parents were very religious and at a certain point I began to see hypocrisy and an us-vs.-them mentality that seemed to be the antithesis of what being a religious person should be about.
On the one hand, I loved many aspects of the church, especially the community aspect, the charitable work and the messages about being kind and giving. But on the downside, there was the judgmentalism that you spoke of.
That said, I know many people who are both religious and fairly open minded, and are accepting of differences of opinion, choice and lifestyle. So it is certainly possible! With my kids, I have focused on teaching them to develop a good moral compass, and to make the world a better place.