If memory serves me right, a rule called PTP Signal/Speed rule used to do that for manual trains. Not sure whether it's in T:ANE though (I last used it in TS12).
Signal Passed at Danger Check Rule - set to trigger every time a train passed a STOP signal.
Driver Schedule Rule - indented as a child rule set to your manually controlled driver, using "Killer" style (so its commands overwrite any existing driver schedule) and then with a simple "Halt Train" as the only command in its schedule list.
You have to specify the driver for the Driver Schedule Rule and there is no way I know of identifying and only halting the driver responsible for an individual SPAD (AI controlled trains should not pass a signal at danger).
What Shane suggests works for me. I can't find the rule anywhere outside of TRS12. Had to extract it into TANE. Why is such a useful rule not also included with TANE?