Going to open a can of worms with this but let's go...

To be honest, and speaking as a former Christian myself, from an outsider's perspective, I don't feel they are off when you think about the tenants. Still Yahweh is not really evil, the game's background points out that God has been warped by something wrong in the universe and it frankly seems to be pointing towards humanity being the culprit which frankly is true to real life as well.

There is also a lot about the angels and Yahweh that has been removed from the faith over the centuries but are placed back in. I mean New Testament God is a pretty cool dude, Old Testament Yahweh on the other hand can be a dick when he wants to be and even his "chosen people" will generally attest to that. I mean it's not like The Books of Joshua, Judges, both Books of Samuel are not rife with Yahweh commanding his chosen people to wipe out every man, woman, child, and livestock that belongs to the heathen's for the sake of Yahweh creating his paradise for his chosen followers. New Testament God isn't interesting, Jewish Old Testament Yahweh on the other hand makes for a very interesting and atypical antagonist.

Granted, SMTII goes a little too far in this regard but the series is not about making religion look bad, as it about presenting people with choices by making them face the best and worst aspects of it. I mean the Law order tends to have more sympathetic characters than Chaos does. The Archangel Gabriel and Satan (not to be confused with Lucifer) are actually some of the sane people on their side. They have actually done a better job of restoring some of the heavenly host back to their place, cause figures like Satan and Metatron kind of got shortchanged by Christianity despite being more prominent back in the day.