Michelle Burns was fired based on what happened when she was principal of Tilden Middle School
The principals' union, which is appealing the decision, called the ruling "a gross overstep."
Three years ago, Pa. officials said 140 educators faced discipline in the investigations launched in 2011. The new administration says it cannot report how many cases are still in process.
The state's largest bricks-and-mortar charter is operated for profit by a GOP power broker. Its test scores plunged in 2012 when security measures were tightened.