It seems like the sensible thing to do would be to fry / erase any IFF and encryption related stuff, but otherwise continue as before.
E.g, if it's already been programmed to fly straight and level, continue to do that. If it's deactivated, stay deactivated.
Just seems like a whole 'nother set of characteristics to test otherwise, as well as adding extra unpredictability. The aircraft is probably damaged / on fire, so its flight characteristics are already going to be extremely different to normal. The best thing in the moment may be to let the aircraft lawn-dart in a field, rather than attempt to get straight and level, and in the process potentially fly over inhabited area or towards a friendly set of aircraft / buildings / vehicles.