It's great to see a show where men are the minority, dealing with real issues and things anybody can relate to - not just stuff that's 'by women, for women'. It's not a chick flick. It's a normal show that just happens to mainly star women, just like every normal show where most of the cast are men.

That's all fine. It reflects reality. It's OK to show the messed up side of religion. It's good even. This stuff needs to be highlighted so it can be dealt with. All the while the moderate and compassionate normal people of faith are also on screen to show that they aren't all nutcases, there should be no reason for viewers to complain.
I don't know the beliefs of the shows writers and producers, although episode 12 seemed to be an example of the main character Piper acting as a voice for their views.
As I say, for the bulk of the series, they've been respectful and handled faith well. The cast includes Kate Mulgrew, who is well known to be a devout Catholic, and also Laura Prepon who is a Scientologist, as well as a number of other people of various faiths, so the producers probably are sympathetic to the belief systems of other people.
So I don't want to come down too hard on the show for the things that were said in Episode 12. It might have been the writers speaking through Piper, or it might have been just another character expressing a poorly thought out world-view. Piper is hardly the beacon of reason and morality anyway - being involved with drug dealers and cheating on her fiancé.
Whichever it is, I'm just a little concerned that what she said might be taken by viewers as good rational sense. So I'm gonna go over it and try to clear up the mess. WARNING: MINOR EPISODE SPOILERS