if they are half synthetic, then could it be that some really ancient race just spread across the galaxy so extensively, that it was starting to over crowd, so the only solution they could come up with was the reapers, so in that extent, as synthetics, they are following orders.
since that race also built the mass relays and possibly the citadel, the race decided to leave false info on the motivation of reapers, and also possibly the plan for the crucible, so that future races have a chance to see the burden that this ancient race has suffered through.
to complete this task, this race would have needed to build fleet of organic synthetic things, and what better way to do that than use the people of your galaxy as the galaxy is already bursting at it's seems. this would have of course started a galaxy wide war. but as the fleet grew larger, the resistance grew smaller.
as a final precaution, this race made sure that an optimum amount of races and people in those races was left, they programmed into them that information, and made sure that their race would always survive, trough similar programming.
once this was done, they destroyed any possible data on this galaxy wide genocide, sent the reapers into their dormant state for 50k years, and wiped their own memory of such an incident, so that the galaxy would never know of this deed.
this is my view on the reapers motivation, and i pulled it all out of my rear, in a sleepy state, so it may have some fallacies