That's a good question and logic I don't think CB thought of. Unless Aleph has been given instructions to always be hands off. Not the same as the Asimov rules. Aleph must let humans fight each other. It could have known it it was going to happen and did nothing to stop the uprising because it's not supposed to be involved in that sort of thing.
While the whole thing is full of logical holes, I think you shouldn't discount the relative competence of the Hexahedron. Additionally, I might be reading too much into that NCA is the only human sectorial that's getting access to the new Shasvastii mercenary. I'm just saying but they're getting access to a Shasvastii...
I'd like to think that the Shasvastii are seeing an opportunity to break out from under the thumb of the EI, and want Humanity to help them... but I may be thinking too deep into double- and triple-cross territory. I really hope that Haqq and Ariadna aren't the 'good guys' of the story a'la the Hyperion Cantos, but that does seem to be the implication.
I think it would be hard for any of the combined to rebel since any of them can be taken over through their cube. The EI sees all, knows all. The new Shasvastii character has a Cube as well. It's because they don't have cubes. It's just a matter of time the Combined just Sepsitor bomb planets to take everyone over.
Yeah, the Shas merc who apparently single-handedly set up the entire uprising. So expect the same in PanO. Also, any game where that Shas appears, if you make it Really Dead (cube fried, dead on the table), you win a moral victory regardless of other victory conditions.