Not even if the Brotherhood said "Hey the Hound is there"? She doesn't know he tried to help Ayra all she knows is that he was an enemy.
That doesn't really matter much as they remain innocent people. As far as I can remember the Hound didn't do anything horrifying in particular against the Starks. Yes he served the Lannisters and abided by their commands, but so have thousands of other people. It should also be a reasonably known fact by now that the Hound defected. So there really is not a single reason for her to command the Brotherhood to kill dozens of innocent people, including hanging a septon. If it was only the Hound she might tried to have him killed for his former allegiance to the Lannisters, but murdering a small, innocent village society? No.
