The point they're making isn't that religion is essentially good until it's corrupted or warped, it's that religioun is a powerful tool you can use to justify just about anything.
Exactly, although in this case, the evil motives which the Priors want to justify really is in line with what their gods the Ori want. So all those scenes in which Vala tries to convince Tomin the Book of Origin doesn't actually say anything about murdering people and being nasty are kind of pointless. Even if Origin doesn't outright say anything about killing unbelievers, we (the audience) know that is what the Ori want. For that matter, Vala was with Daniel when he communicated directly with the Ori, not to mention her own daughter is an Ori incarnate, so she should know the Ori really don't have a problem with being a douchebag, even if their scripture leaves things open to intrepretation. So while I get the message the episode is trying to convey, it's one that has no real relevance to the Ori storyline. It really doesn't matter how you intrepret the worrd of the Book of Origin, the Ori are villains and encourage their followers to do villainous things.