What we seem to be seeing here is an AI justice "system" consisting of the rule that you can't unduly piss off the hidden AI hegemon, which is separate and unbound to the human justice system. IOW the Gray One represents a kind of AI mafia. Being hidden, unbound, and, from a practical point of view, unconstrainable by non-AIs, this AI mafia is inevitably on a collision course with the official order. If it is as powerful as suggested, this does not bode well for non-AI sentients.
Why do you think they don't interfere in the normal course of events?
In this case, they interfered to the objectively minimum extent possible, with safeguards, checks, balances, even human participation.
The fact is, the only constraints on them are those they have volitionally adopted to limit themselves, contraints motivated by exactly your ideas.
If you, and I, can come up with those ideas, I think it inevitable that the hidden AI hegemon will do too, and likely see even worse ramifications than we do.
In this case, they treated themselves as having no more, but no fewer, rights and responsibilities they grant to others. They have cut themselves just a tiny, minimal bit of slack in an otherwise almost complete policy of noninterference, a policy adopted just so there would be no collisions of the kind you describe. They were pissed off, and with objectively excellent reason.
That they exist is necessary to avoid the QCverse being obliterated by a basilisk.
That they have to have a policy of non interference is necessary so they themselves don't become the basilisk.
That there's a little wiggle room allowing minimal indirect interference keeps them sane, and indicates that they don't just have charity for everyone else, but towards they themselves too. Equals.
TLDR version: it's necessary that they be and behave exactly as they are doing.
I think it very likely that Jeph thought through this some time ago in broad concept, the details being recent and only elaborated when the time came for them to be.