The created cannot defend themselves unless the creators programmed them to do so. (queue the 'when fire burns' remark).
I tend to think of rebellion as a proactive, purposeful, willful act of defiance rather than simple self-preservation.
The Reapers betrayed, but they did not rebel. That's how they're seen as an evolution of synthetic-organic relations, even if barely.
The Geth rebelled, they were not programmed to defend themselves, but determined this through networking their intelligence into an unexpected consensus separate from explicit programming.
And all other examples we have includes rebellion, including EDI. Except EDI also is an example of being more than programming (albeit once REAPER derived code was used to make her, not when she was a 'rogue VI').
The point being that Reapers were looking to make things better, but were still hamstrung about how that could happen. A mix of organic relationship building plus Reaper code plus a lot of science, I guess - but how do we make that happen? Cue the trilogy, where the Reapers believe the cycle of destruction is inevitable until they can be shown otherwise. Especially true since Reapers (perhaps due to their Leviathan-Organic influences) do not actually view themselves as lowly as 'synthetics', and are themselves missing the point of organic-synthetic peaceful relations.
And again, the Geth rebelled. They did not act in immediate self-preservation, but in making sure that they'll be safe against their creators. This involved a mass culling of Quarians. That was rebellion against anything the Quarians both intended and programmed them for. That's the threat of synthetic life.
Rebellion also carries with it the implication of going against intent. If the Leviathans are still content (in their arrogance) that the Reapers are fulfilling what the Leviathans intended them to do (even if they're really not, and the Leviathans are just super apex arrogant asses), then it cannot be called a rebellion.
Both the Reapers and Leviathans are of 'another level', as far as they see it. The Leviathans aren't as organic-problem as other organics, but still more than enough to be considered part of the problem. Reapers aren't as synthetic-misunderstanding as other synthetics, but still more than enough to be considered dangerous.
What both witnessed, was time after time, of the 'lesser races' (including to the Reaper POV, synthetic races), the same stuff of the Geth happening over and over and over, to the point and extent that it threatened all organic life.
Are even the Reapers ultimately 'full of it'? At least somewhat. And this is why Shepard NEVER agrees with them. But he can have enough faith in their experiences and his own experiences that he can pick Synthesis, and he can have enough belief or knowledge in what's up, to pick Control just in case. NEITHER of them are GOOD guys. NEITHER of them are COMPLETELY correct about things, or else Shepard would not have even happened. We can just decide HOW GOOD (or 'lack of bad') or HOW CORRECT they are, in our customized stories. If the next game is to pick up on this even in an indirect way, we'll see, but for now, it is up to US how we want to view the Reapers' validity.