Dogma/WMG

Loki and Bartleby were indeed forgiven and allowed back into Heaven.
Loki certainly redeems himself at the end. And God said it all with that loving embrace -  doesn't really need words to say it any more clearly. Allowing them back into heaven arguably wouldn't cancel out existence - it doesn't prove God is WRONG, it proves God's infinite mercy. The sort that to this troper, is the only way the world makes sense.
 * Many would say that God said, back in the day, "They will NEVER be allowed back in," and, thus, they can't. But theological history has shown that God can change "His" mind, so if Bartleby was forgiven at the end (which is NOT expressed by a hug; that could have just been a 'there, there') he could have been allowed into Heaven because God changed her mind.
 * Another idea that as Angels Loki and Bartleby can never return, but as humans God can allow them back in.

Loki and Bartleby's exile to Wisconsin was never intended to be permanent.
It was actually a Secret Test of Character. Bartleby thought he knew better than God (sin of pride) and convinced Loki to follow him. God wanted to prevent another Lucifer incident so exiled them to earth until they showed humility. Trouble is Bartleby is too proud, and Loki too easily led, to apologise and admit they were in the wrong.

Loki eventually passed this test when he tried to stop Bartleby killing Bethany and was forgiven and let back in not proving God wrong, but proving God's compassion. The same happened for Bartleby when God confronted him at the church and made him realize the true ramifications of all his actions and genuinely asked for God's forgiveness.

Metatron is Lucifer's twin.
No real proof for it, but something to ponder.
 * Well that certainly fits under wild mass guessing.

The events of the film are all a part of God's Plan.
With the end goal being presumably to restore Bethany's faith and set her up as a proper mother for the next incarnation of the Saviour. This explains why God was so easily dispatched, why the Metatron felt the need to call for Bethany's help yet never intervenes himself, why nobody seemed to understand how plenary indulgence actually works, and why none of the other millions of angels in God's service, many of whom exist for exactly this sort of occasion, ever get involved.
 * I hope Kevin Smith is a Troper, because this would be the perfect premise for a sequel.
 * Wait, wait.... there's millions of angels who exist for the exact occasion that God's been kidnapped while playing ski-ball and the stars of Good Will Hunting go on a killing spree while trying to get back into heaven which will destroy everything everywhere forever?
 * Yes.

God is Alanis Morissette
Like, the Real one. Meaning God doesn't understand Irony, making the Bible make much more sense, if you think of it as God trying to be Ironic.

Bethany has a special protective aura around her.
Which is why Bartleby didn't know she was the last scion until she told him. Who had the foresight to put this aura around her? Metatron, of course. If Loki or Bartleby crossed paths with her, the plan to rescue God and save the universe would fail, so he took extra precautionary measures.

God is Haruhi.
Seriously! Just look at how she acts! Which I suppose would make Kyon as Metatron.

Dogma was the reason why the Clerks cartoon was canceled.
See The View Askew Niverse

== The reason Loki and Bartleby were willing, or even able to be willing to go against God's direct, unfiltered orders was because the message was clouded by their living memories after God didn't use the big voice and they didn't personally get to chat with God for a long time. == They may have gotten the message passed down through Metatron if they were on earth (in Wisconsin) when the exile was explained to them, or God has a business voice that specifically filters out all the cool and potentially earth-rending stuff that the Vox Dei can do (such as the voice that got put into the burning bush, or talked to Abraham and Noah). At the end, God  results in him realizing how much he messed up, which is because he'd been reminded of how amazingly, wonderfully, freaking awesome God is, the way humans are supposedly incapable of not exalting God once they're in "His" official presence, free will and all. If they had been banished to a really sucky corner of heaven, or to a commune of people who really, really love God and aren't afraid of showing it, they never would have thought about disobeying for more than a few instants at a time. "Metatron: Anyone not already dead or from another plane of existence had better cover their ears."
 * I sorta thought it was because, y'know... they were angels? Metatron's head didn't explode when he was RIGHT NEXT TO HER in the ending, so why should it be any different for Loki and Bartleby, so long as there weren't any other humans around, they should've been fine. They were banished, not turned human.
 * Two things: First, it's only humans that can't withstand God's voice. Remember Metatron's warning:


 * Second, Loki and Bartleby are like Satan: they're banished angels. Satan went against God's will and didn't apparently have a lot of trouble doing it, and indeed all those who followed him into Hell didn't have any problem doing it.

The reason Bartleby and Loki were banished to Wisconsin is because, in-universe, it shares the defining aspect of Hell
God's presence can't be felt in Wisconsin. No decent skee-ball machines.