The problem is the geth are self aware, like any of the organic races you encounter in the game (not counting things like varren, mind you). However, unlike organics, I doubt the geth have any reason to lie about anything, and perhaps not even the capacity. And even if they did, that would be further proof of sentience, which makes them have an equal right to existence of any other species.
The geth were not hostile to the quarians when the quarians tried to wipe them out, they were merely trying to come to terms with their existence. The quarians had a knee jerk reaction, assuming the geth wouldn't be happy doing dangerous or menial work for long and would revolt. I personally think that's a load of horse dung.
For example, Legion informs Shepard that the geth have maintained the quarian homework, including all of it's utilities and functions that the geth have no use for, when they don't even want to particularly live there forever. They just want to be left alone in some quiet corner of the galaxy making a Dyson Sphere for the geth to live on independently. Even if the work was dangerous to individual geth frames, losing a frame is like clipping toe nails, because they can upload their individual platform into the network or another frame, as long as they were in a network with other geth. For example, if Legion dies in the suicide mission, it actually dies because it's last words are something akin to there's nowhere for it to upload it's platform, so it dies in the body. My point is, you can't compare our values and understanding of the world to theirs, as many things don't directly apply. From what the series has presented us, one of the main reasons the geth want to be isolated is that they want to study and learn how to coexist with organic life, as they are afraid of being wiped out by another misunderstanding.
So, if it isn't possible to help both sides of the conflict, I'd rather help the geth. They are in the right to continue to survive, and the quarians are being the foolish aggressors. I'm pretty sure it didn't occur to the quarians diplomacy with the machines that still view them as their creators is always an option.
Besides, in a fight, the geth are infinitely more useful. They have greater numbers, better technology, unity, and they aren't going to die of disease if their bodies take the slightest bit of damage from some stupid infection.