I really don't think the Overlord is "God" (He doesn't act like the biblical God at all. Even Old Testament God doesn't specifically target innocent people.)
Pretty sure Agito's mythology is an interpretation of Gnostic theology instead of traditional Christianity. A lot of stuff about Gnostic belief was published for the first time in various languages around the time Agito was made.
In Gnostic belief, there's a good God and an evil God (sometimes considered Satan if you're dealing with Gnostic Christianity) who are equal in power. The good God created the human spirit, but the evil God created the material world and human flesh (and this is why evil exists).
The point of human spirituality in Gnostic terms is to reject the material world and embrace your true spiritual nature. By striving against evil and making your spirit stronger, you can hope to break free of your corrupted flesh and, upon death, join the good God in the spiritual "realm of light" he was thought to exist within.
Agito spoilers ahoy! [HIDE]If you apply this theology to the plot of Agito, then it seems to me that the Man in Black is the evil God, and the Man in White was the good God. In this mythology, the evil God was able to overwhelm and "kill" the good God. Of course, something that's infinite and immortal doesn't really die. Instead, the good God was broken into fragments that joined human souls, and those with a fragment and a pure soul could become an Agito like Shouichi. If you had a fragment and were less than perfect as an individual, you might be Gills at best and Another Agito at worst.
The Man in Black sent the Unknown out to hunt down humans who could become Agito because he didn't want his creations to gain a power that could rival his own. And in Gnostic thought, the evil God sends demons and other minions out to try and make people corrupt, evil, and more "material" in nature, so they don't escape his power. The show ends with Agito kicking the Man in Black to represent humanity transcending his influence and choosing its own destiny. The epilogue seems to imply that, given enough time, everyone may become an Agito like Shouichi. [/HIDE]