Have a character that makes it clear that one can be a good person and a member of the faith and that the trouble with "religion" she has are people who take it too seriously. As someone who had my own crisis of faith with the Catholic Church, my problem was not with the priests... it was with some of the lay community leaders who were taking things too seriously. I never had a problem with the priests and was good friends with one priest and talked with him about matters of faith as much as matters not of faith. (One of my pet peeves about religion, especially certain sects of Christianity is the evangelicalism or active recruitment of people to your church. I've always gravitated to a more private and quiet relationship with God.).
There are plenty of religious people who are... just people... it's clear that they are into their faith... but they aren't into you being into their faith unless you want to.
I would also, if you fancy a trip to the black hole that is Tvtropes, look up the trope "Jesus was way cool" which is a trope that focuses on the fact that most of the problems with a religion aren't the fault of the divine but the fault of the humans. Some of it is critical of organized religion... but it's from a point that even if you have a problem with a church organizations and rituals, Jesus, as portrayed in the Bible, is still a bad ass and said some pretty important things and was pretty chill. For example, Jesus' first mirical was saving a wedding party by turning water into top shelf wine. How many other religions have a god who's first miracle was "to bring the good shit to keep the party rocking?"
Have a character who can show her that it's okay to have faith... it's okay to be part of a faith... and not be an ass about it. Or more daring, and I know they exists, have a character who doesn't believe in a religion... but still thinks there are some important lessons in the Bible and doesn't discount it as a work of literature (I'm aware of a guy who is not a Christain, but still keeps a picture of Jesus in a place of importance... according to him, Jesus was a guy who went around and helped people and he likes those types of characters.).
Yes, there can be a lot of people who are religious and are jerks. There has always been in every human organization more supply of jerks than demand. Religious institutions are no exception. But for every jerk, there are 10 people who mean well and live their faiths.