Legion does speak of "true unity" and transcendence (here's the link again:
http://www.youtube.com/watch?v=CqtAHNQT3-w ). It's not explicitly stated as such, but all the leads are there. The Reapers just eradicating synthetics wouldn't help over time. As we've seen in our own world, all it takes is 10-20 years, and then all lessons of the past are forgotten. Letting civilizations evolve and hit their golden age, and then harvesting them, would preserve their culture and their people as a form of super-being, housed inside a Reaper. And they wouldn't have time to invent synthetics with the ability to kill every organic being in the galaxy.
Interesting thought really. Every time a Reaper is killed, an entire civilization is lost forever.