Dull predictable episode and ending. An man Brian was a fucking douche in this episode. Granted I'm not big cheerleader of religion, but come on Meg found something that made her feel accepted and loved, they could have dodged the easy shots about book burning and bashing on religion and just ended with Meg being religious and that's that. Taking shots at religion is easy, too easy and unoriginal.
They weren't taking a shot at religion, they were taking a shot at ORGANIZED religion, and more specifically pushy Evangelical Christianity. There is a difference between "I believe in God" and "I'm a Baptist/Catholic/Lutheran/Methodist/etc." I thought that was made pretty clear when Lois seemed aghast that Brian didn't have any spirituality, although she had no problem with his lack of affiliation with a religious denomination or lack of church attendance.
And it was specifically targeting pushy Evangelism, as personified by Kirk Cameron. Read the real life story behind Kirk Cameron and his "conversion" to Evangelical Christianity. After his "conversion", he became a pushy asshole who demanded that everyone else conform to HIS newfound religious beliefs. He even had the audacity to use his star power to demand script changes to make the show more "Christian." And we see that by adopting the "Kirk Cameron" Evangelical form of Christianity, Meg becomes a pushy asshole as well who insists that her family conform to her religious beliefs.
It wasn't a slam on all religion, or even all organized religion, but more specifically on one form of religion which is personified by ignorance and intolerance.
And FYI, Brian the atheist is also portrayed on the show as an alcoholic, so it's not like they are really holding the atheist character out to be superior to the religious characters.
Don't forget that Peter Griffin is Catholic and the family does occasionally got to church.
Oh and there was the issue of Peter's father objecting to Lois because she wasn't Catholic.