My Theory:
The physical reapers (the giant robot space squids) do what they do because they are warped and twisted by their creation. They are meant to preserve organic civilizations but they do it in a manner they were created: twisted by fear and terror. Basically, reapers are made from slush of millions (billions?) of organics, and those organics died in terror in the face of an almost unstoppable foe. So, basically, the reapers are the terrified, warped, twisted consciousness of millions of individuals but only giving the outward appearance of cold, calculating space squid robot dreadnaughts.
The actual original conciousness behind the reapers, who takes the form of that fucking annoying kid, is actually the product of the very first advanced organic civilization in the galaxy. Because they were the first, they had the run of the ENTIRE galaxy. I mean all of it. Their technological power (they created the mass relays and every bit of technological superiority the reapers have is because it came from them) was immense, getting the stage where its almost techno godlike. But because they were the first and only race in a young, still forming universe, they were alone. And so they threw themselves into creating an artificial life of their own.
No their creation didnt rebel, it was exactly as it was intended to be. The entity/s that spawned the reapers eventually essentially started out as fully independent, free willed synthetic life. They found purpose with their creators and it was all completely harmonious. As time passed they began to evolve and become more and more entwined with their creators and it slowly started to coalesce into the galactic consciousness behind the reapers. basically it was a machine intelligence that covered the entire galaxy, linked to the entire race.
Then a series of events brought about the original races extinction on a galactic scale. You know, multiple cataclysms and pandemics and all kinds of shit brought about the essential premise that all things come to an end. The reaper conciousness endure however and was fundamentally scarred by the extintion of its creators, and because it was essentially one with them, that basically sent them mad.
Yeah, okay its that shitty insane AI principle, but its my own personal way of trying to rationalise the insanity, the stupidity, the delusion behind the reapers, but also the technological advantage.
Its also, on a reaper space squid armada level, my way of trying to explain why for a race of giant space squid robot thingies with a supposedly benevolent motive of protecting organic life, they achieve this through sheer nightmarish terror, excessively so.
The reason why the reapers are so cruel and sadistic and excessively nightmarish is because their foundation that gives them "life" is last thoughts of a terrified now dead population turned into liquid. That they are tainted by their creation.
So yeah, insane, misguided galactic consciousness from near the dawn of the universe spawned by the very first advanced organic species in our galaxy, who has spawned an out of control insane robot squid armada that recreates this delusional cycle over and over.
Its a shit, nonsensical reasoning, but I figure its no worse that Biowares and has as much right to be the in game reasoning.