It's also good to remember that in this version of the world, the LP's been in power for 11 years or so - it's entirely possible he (or someone else) was checking on Minerva regularly for a while, but she's been so above suspicion for years that the checks are now fewer and far between.

Also, one wonders what the functional protections are on Hogwarts - there may be stuff that even the LP/Bellatrix/whoever can't easily bypass.

McGonagall's long been my favorite character, and one of the things I'm loving about this is getting to see more of her private thoughts (and public actions). Even if she's also breaking my heart.