I see why you question if it's rebellion. The Geth did acknowledge the Quarians as their authority and willingly served.
Well - they were essentially machines until they gained self-awareness. Once they did gain self-awareness, did they see themselves as slaves to the quarians, or accept quarian society as their government?
They followed all other instructions even asked how they could do better when told to shut down.
While it might be there, I don't remember that. What I remember is geth asking if they'd done something wrong when told to shutdown. It might sound like nit-picking, but I think the difference is important. I'm not expected to please my local government authorities (or random strangers) in my day to day activities and choices, but I'd expect to be apprehended if I actually broke the law.
The Quarians saw them as tools, not people. Whether or not they had the moral authority is irrelevant to whether or not the Geth rebelled, only to if that rebellion was legitimate.
The quarians had very mixed opinions about that - not only in the memory chunks we were shown, but even 300 hundred years later. The Admiralty Board is far from unanimous in how they want to deal with the geth.
For the Cerberus example, it would be if it was a conscious decision to not commit suicide, but not if they attempted and their means to do so failed.
It depends, I guess, on whether you see suicide on capture orders as having any sort of legal or moral authority. I'd say they have neither. I think one could also argue that once captured, the individual is no longer serving as a Cerberus employee and thus any conditions surrounding that employment become irrelevant.
There is no evidence that the Geth couldn't shut down because of some self preservation routine. Not only does Legion "off himself" to ascend the rest of the Geth, but in one of the historical records, we see a Geth unit offer to give itself up to the Quarian police or military in order to protect its master.
Don't you suppose that self-awareness along with the ability to think for one's self would override whatever logic they'd had that caused them to prioritize input instructions from other sources? Legion and the self-sacrificing unit acted of their own volition.
But just for kicks, let's look at some definitions of rebel:
-- to reject, resist, or rise in arms against one's government or ruler.
-- to resist or rise against some authority, control, or tradition.
... which brings up another question.
If an otherwise law-abiding citizen chooses to break a specific law or not immediately comply with a specific instruction, is that an act of rebellion?