Well they could be indoctrinated like Saren was, or believe that if serve they will be saved, similar to the keepers on the Citadel
From Derint: Reapers use organic races as pawns and tools to achieve their aims in the short term even though their long-range goal is to exterminate all organic life. It's a case of practicality being more important than strict adherence to philosophy. And note that events and dialogue in ME1 insinuate that the Reapers view the geth - despite their inorganic nature - as useful at best, to be discarded when that usefulness is at an end.
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