In general the empire and all feudal systems have far far less centralization of power then we take for granted in the modern day. In effect most people are acting without oversight because there just plain isn't nearly enough oversight to go around.
If anything, that supports the idea that the Grey Order
cannot and also
will not act as some kind of unofficial, highest-level oversight for the Empire or its Elector Counts. Its job is fundamentally geared towards "enemies of the Empire", and not in the metaphorical sense. It focuses on illegal cults, Black Magisters, nobles going so corrupt as to be in clear and egregious violation of the law (to the detriment of the Empire on a significant scale), as well as stuff like the typical undead, greenskins, beastmen, etc..
The only reason Regimand went on a murder spree was because he had solid proof--corroborated by the Witch Hunters, no less--of specific people directly and willfully involved in a Lahmian conspiracy aimed at the Empire. That the Empress-Consort was on the list meant that she had to die because she was a traitor--and that the Witch Hunters didn't do it themselves was because they didn't want to take the political heat for the act, but the Grey Order is explicitly obligated to act regardless of the risks to themselves.
Even then, the way the Grey Order handles things like that is deniability and responsibility. Should a Grey Magister ever come to the conclusion that assassination is the least bad option, they take the matter upon themselves knowing that they have to take the secret with them to their graves, with no reward or thanks, because the leadership
cannot be okay with it. And since performing such an assassination is a very risky endeavor (if you get caught, you will be thrown under the bus and you will be expected to assume full responsibility for it even as you burn at the stake) and no reward is expected, the only reason to do it is the heavy weight of duty and necessity.
When Boris asked Mathilde for help, before she agreed, she asked what he would do if she refused, and he basically answered a coup or civil war, acknowledging that it would be awful and costly. For Mathilde, the answer was clear: it was better for the Empire, for Kislev, and for the world if a civil war in Kislev were avoided even if it meant putting herself at massive risk to make the attempt. She can't let anyone other than Boris himself (who already knows) ever know that she did it, and the price paid was for the benefit of the Empire and Kislev rather than herself (or the Grey Order's). Algard and the other LMs have to not be okay with the act.
This is the ultimate form of Grey Order self-limitation: the very means it could use to exert control over the Empire that it is supposed to serve are utter taboo beyond a very personal, individual level; without reward or aid and with tremendous personal risk. No conspiracy can be created, no coordinated strategy or effort can be made, so even your fellow members of the Grey Order must not find out what you have done lest they be forced to take you to task. It is inherently self-limiting.
The Grey Order isn't oversight for bad leaders or unfriendly-to-the-Colleges leaders. It's oversight for illegal cults and actual traitors.