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People keep making the mistake of labelling the Reapers as machines. Asides from the fact they're all giant spaceships, there's no reason to think they are machines, at least in the conventional sense.
The exact nature of the Reapers is not elaborated upon at any point in the game (I would consider this a plus, not a minus myself...). We only really have two hints:
1. The Geth called them "the Old Machines", I don't think this means much, it was convenient to Sovereign for the Geth to think of him as a fellow machine.
2. Reaper manufacture is shown to require turning organics into Tang, and constructing some kind of metal exoskeleton.
My hunch is that the reaper is a large brain or something using the tang, surrounded by a metal exoskeleton and weaponry, used to protect it.
Even if they are machines, they're not programmed in any conventional sense. Reapers have their own free will (albeit one subservient to the Star-Child).
The reapers could have any number of reasons for wiping out life on a regular basis, the stated reason of "organic vs. synthetic" is silly, but you could think of any number of reasons.
But frankly, the Reapers don't have to justify themselves to us. It's like God in the Book of Job. In Job, the question is asked "why does god allow bad things to happen to good people" and the answer is "God does not have to explain himself, he does not have to justify himself". While it is unsatisfying (as it dodges the question), it is true.
The reapers don't need logic for their actions, they just are.
Unfortunately, Bioware felt the need to explain their galactic plan, I say Boooo. The reapers don't have to explain themselves to puny mortals like us. We simply must obey or die.
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