What if an alpha core put in as an admin started giving you occasional 'missions' in exchange for its services and you had a relationship bar to cultivate with it, too, like personal contacts? I have to admit that I, too, think "Kill all humans" AI isn't necessarily the most interesting, nor did I ever really get that feel for that being how it things went down in-fiction either; the AI wars are so named for Tri-Tach using AI fleets, rather than all out AI uprisings against humanity, right? Did I understand it right in the end? Given how alpha cores are superhuman, might well know they're superhuman and start cultivating their own designs and quirks, these missions/requests for continued cooperation could be just about anything pulled from the pool the game currently has (Alpha Core works in mysterious ways, right?), perhaps themed to some preset grouping depending on a 'quirk' the AI core might get assigned upon getting slotted in, and then you could have the "all out AI uprising" as a consequence for the relationship falling to hostile through just consistently ignoring them rather than a statistical inevitability/chance.
And if you happen to use multiple Alpha admins, well, they could presumably communicate behind the scenes and present their (Combined? Unified but more onerous? Both?) 'requests' in unison, with the understanding that, of course, should their requests be ignored, they will have to do something to redress the situation together...