Blind obedience is pretty weird, especially since Palpy has just turned into scrotumface and looks nothing like himself. And the Jedi have been fighting alongside them the entire time. As their officers!
I mean... practically all governments have legal structures for emergency decrees et cetera, but suppose: it's near the end of the American Civil War. The Confederates are on the ropes. Suddenly, Lincoln sends out a message to the rank-and-file soldiers, saying: "I've just signed an executive order. You are to summarily execute all your commanding officers immediately. Yeah, I mean Grant and all the others. Kill them all. Do it now."
Also, he's suddenly got grey skin, is weirdly wrinkly, and his eyes are kind of glowing yellow.
Do you think... that they'd go and do it? Like, right away, no questions asked?
Or that maybe, just maybe, they might ask some questions and figure out what's happening here?