Conversations with the geth programs dubbed "Legion" have brought to light a profound schism in geth society. When Saren Arterius approached the geth in the dreadnought Sovereign, some of them chose to follow him; most did not. Saren's followers were allowed to leave geth society, but were dubbed "heretics" by those that remained.
This revelation implies several things. First, the majority of geth chose not to attack organic society. Second, the geth forces the Council and Alliance fleets have battled the last two years represent only a small portion of their actual military and economic power, perhaps as little as five percent of mainstream geth society. Third, this schism suggests that individual geth possess more free will and perhaps even personality than previously suspected. Without such individuality, no geth could have deviated from the group decision to join or reject Saren's mission. There could not have been a division.
Finally, there is the matter of Legion's word choice. The geth used the English word "heretics" to describe Saren's followers. Of the many words Legion could have chosen (nonconformists, dissenters, rebels, etc.), only the word "heretic" suggests a broadly accepted geth philosophy or religion, and that the actions of Saren's allies violated the orthodoxy.