I'm with you that there's often too much alienation of religious folk and maybe there's a better way.

Past and current socialist countries have had to contend with religious organizations not because of the beliefs they hold, but because of their organizational capacity. The Orthodox church for instance previously was a bureaucratic wing of the imperial Russian monarchy, responsible for things like the census and education. There are a bunch of Soviet posters focused on getting young women into schools, whereas previously they would have been made into nuns.

China similarly had to contend with the Catholic church as a vector of colonization and foreign money, which is why China still has no Vatican approved churches, but rather, there's an internal Chinese Catholic church administered by the state. Same thing in Cuba, the churches ran the schools, and that's simply not something a democratic society should have.

I think there's a trap where religious belief and religious organization are conflated as the same thing, when they aren't. Religious belief can't be grasped nor directed, I don't think it's possible to fully extinguish nor should it be. People are gonna find things to worship or find an afterlife to chase, that's normal and part of humanity. Big organizations with ties to state powers is where stuff starts to get confusing.