Livin' on a Prayer is by no means a typical episode with religious commentary - this is a surprisingly effective and intelligent episode, that I think any Christian should sit down and watch. Because I don't have any problem with a criticism of religion - it's when there seems to be no point or message, but to anger Christians that I truly find myself offended.
In my opinion, if you are going to criticize a religion, then you need to really have a reason for it, because if you're going to just hate on religion, then there is no reason for anyone, even atheists to listen to you. The same can be said about Christian movies, that caricature atheists as evil, unreasonable jerks.
In this episode, Stewie's new best friend is seriously ill, and his Scientologist parents won't give him treatment, because they believe that praying for a cure is the answer.
There's a rather funny scene where Lois and Peter have to kidnap the boy in the middle of the night to send him to hospital, without waking the parents.
At first, this episode doesn't tend to be anything out of the ordinary, but it's what Lois says at the very end that truly makes this a special episode. She says that For thousands of years Christians have been praying for cures of illnesses, and that the scientific medicines that have been created are an answer to their prayers.
Whether or not this was intended as a pro-religious episode, rather than alienating the people they are criticizing, they are speaking out to them. Rather than condemning faith, it is condemning a flaw of faith, as any truly good commentary should.