How about the Reapers are actually doing the galaxy a favor. If left unattended, the galaxy inevitably blows the shit out of itself so hard that the purpose of life is ground down to basic survival, which in itself is an awful, day to day existence. So the Reapers are like, "Hey, Shepherd. Dude, you can like kill us but you'll only be causing horrible pain in the end. Or we can wipe everyone out and a new generation can, in time, enjoy life the way it was meant to be even if it is only for as long as we allow it." The realist vs. idealist choices are well overdone, but I like 'em.
Whatever. It would not really surprise me that the BioWare writers themselves have no idea and instead are scouring the internet for topics just like this to find some way to wrap up the hole they dug themselves into.