I honestly don't get why the religious groups would have a problem with agent of God being brought into the show. I mean... they're angels and don't the religious Groups believe in angels?
Personally, I'm happy that the concept of the "Other" side is FINALLY being explored. Up to this point, most of the demons themselves (low on the totem pole mind you) have had no real clue if God is real or not. They're just agents of Chaos for the most part. Human souls that made bargains or deals long ago and then eventually slipped into becoming Demons. No one we've met has really been one of the Fallen yet.
Anyways, I'm looking forward to seeing what happens now. I'm hoping that the Archangel is legit and NOT out for some nefarious purpose, but again we'll just have to wait and see what happens next.
Also, just to add:
Sam shouldn't be lying about his powers, BUT I think Dean's kneejerk reaction to his abilities is the reason for it. It's very possible that someone with "Bad" powers can choose to do good in a universe where there is Free Will, but then again Absolute Power corrupts more often than not.