Hi Wanderer:
Interesting question.
My mother was raised in a cult but was kicked out when she married my Dad, and yet almost 50 years later, there are still things that bother her. I know that she struggled with stuff as I was growing up and it led to anger, depression, and suicidal thoughts at times. On one rational level, she knows they were wrong, but inside the feelings are in conflict.
I think Blondie is right about examining beliefs to see where they come from and then either owning them or not. As a Christian, I believe that the holy spirit will renew our hearts and minds if we ask, but we also must examine beliefs to make sure they are biblically correct. I think too that it helps to have someone who can help remind you about this if you start to slip into old thinking patterns.
But if you have become an athiest or agnostic, you'd probably want to check out a deprogramming group or book or counselor or something. I don't think we can underestimate the powerful effect of brain-washing, especially when it starts so young. The posts on this board testify to that fact.