I picked up on a strong theme of anti-AI sentiment amongst organics throughout all the ME games, the setting is very similar to (and gives a few nods towards) Frank Herbert's "Dune" and Iain M. Banks "The Algebraist", both of which have strong cultural and legal prejudices against sentient machines. As they (and Isaac Asimov) are amongst my favourite authors I always like to explore the relations between biological and technological life, and the handling of A.I. by organics was certainly the "something wrong with the universe" that you find in cosmic horror like ME.
As the Geth were monitoring organics they would be well aware that popular sentiment amongst people and leaders would prefer to see them eradicated. Whilst there is no way of knowing what the Geth would do post-singularity it would not be unlikely for them to make a pre-emptive strike to ensure their survival, or even wait to be attacked and then wipe the floor with organics. The rogue-AI on the Citadel was well aware of this attitude which is why it chose suicide rather than discourse (and tried to take Shep with it).