The plot of the movie was God's plan all along, as evidence by Dennis Quaid describing how he bought the diner there because he just 'had a feeling' that it would become important. It's played as a subversion at first, until Michael explains that Jeep always had been the Child's true protector.
Combination of this and a Fridge Horror entry below: The Legions of Heaven seem to be set on a way of thing similar to that of Lucifer's. This could be why God ordered the descent and extermination of humanity: he wanted to test his Angels to see not only if they were blindly following his orders, but also to see which angel's way of thinking needs to be changed and thus where to act. Exterminating humanity also wouldn't be that devastating, as in the Bible God is perfectly capable of bringing the dead back to life. It reasons to believe that had the Angels actually been successful in exterminating humanity outright, God would probably just reset everything with His power.
It's shown that even as a human, Michael is a near-equal match to Gabriel, and when restored to an Archangel he's able to easily defeat Gabriel in combat. In the Bible, Michael is the chief of all angels and archangels, does battle with Satan himself, and is appointed as the guardian of Israel. Of course he would be the best fighter amongst any of the angels.
One might be wondering as to why God would send the Angels out to exterminate humanity instead of just destroying them via another flood. Other than the fact God doesn't actually want to exterminate humanity, it can be justified as God did promise not to flood the Earth again.
With the exception of Jeep, Charlie and Michael, every other character that died wasn't resurrected. Since they were killed while they were going against God's will, they're probably in Hell, suffering for all eternity because they were fighting for their lives and protecting a pregnant woman from blood-thirsty monsters.
The Legions of Heaven's mentality, they are a bit too eager to descend and slaughter humanity, as well as kill the newborn Saviour of humanity (who is implied, in the movie at least, to be a kind of "Fail-safe" by God to stop the Apocalypse), this implies that most of Heaven's Angels are a lot closer to Lucifer's way of thinking towards humanity than Michael's.
