If a drone is being teleoperated by a human, you are still, essentially pitting a human against a human, and the pilot in the cockpit of a fighter has much better visibility that a teleoperator depending on a drone. A small, local EMP generated by a fighter air craft, especially if directed, is not going to hurt the hardened electronics of that aircraft. Drones, of course, could be so hardened, but then they become heavier, mitigating one of the advantages of a drone.
The advantage of a human pilot, as i mentioned, is in judgment of the situation on had. Here's a case in point. At the beginning of the Gulf War in 1990, Iraqi aircraft flew off to Iran or Syria, to land there in an attempt to conserve the Iraqi air force. A pilot on the scene could have seen this mass exodus (and, in fact, they did), and turn aside to go after other targets. A drone on AI is not likely to understand that, and give their limited visibility, it is unlikely that a teleoperator would immediately recognize the situation. A teleoperator is not able to turn his head in a cockpit the way a fighter pilot is able to do.
A lot of this discussion is moot, though, since it is principally the United States which uses drones, and our targets are in places like Yemen or Syria where there are not sophisticated defense systems and little likelihood of retaliation. Where you fight and whom you fight matters, too.