You know, the more I think about Miss Minutes, the more terrifying she becomes. Sure, she can't "do" anything physically, but. . . by all appearances she is an intangible, indestructible AI that can appear anywhere and anywhen, and knows pretty much everything that her creator does. The Time Keepers may have been the big obvious means for controlling the TVA, but I'd bet Miss Minutes did the vast majority of the actual work at doing so.
( For that matter, how much do you want to bet that Miss Minutes managed the Time Keepers, too? )