Nothing in the aircraft's flight control system or computer can interfere with the mechanical arming and firing of the ejection system. Both pilots could have punched out at anytime.
On any fighter aircraft, the pilot still has to physically hit the Weapons Select switch, flip the Safe/Arm switch and then physically squeeze the trigger on the joystick for a missile or gun to be fired, or a bomb to be dropped. Even if the fighter was a totally fictional "F-130", the US Department of Defense would never procure a combat aircraft with a computer-controlled hackable system where an outsider can cause the aircraft to launch a weapon for exactly that reason.
Air-to-air missiles have a minimum range at which they can be fired so that the warhead can arm without blowing up in the face of the launching aircraft. At the range at which the lieutenant commander's plane fired at her wingman, the missile either would have hit the wingman as a dud and gone ballistic after impact, or have gone in front of the wingman and blown up somewhere in front of him. If it had detonated in real life at the range it was depicted on the show, both planes would have blown up.
Letting the fighter's fuel burn down to empty to flame out the engines, so that Team Scorpion could reboot the computer remotely, makes absolutely no sense. The electronics will keep running on the battery bus as long as the batteries have any power. And then restarting the engines after the reboot and pulling out of a 90 degree dive, so she can go on her merry way back to home base? ON WHAT FUEL???
Sub-launched nuclear missiles do not make sharp left hand turns in flight.
From the time the Valkyrie buzzed Sly and the bad guys, it is physically impossible for the pilot to turn the plane around, land and run about 1/4 mile to help Sly in about 30 seconds.
In ICBM silos and on Ballistic Missile Submarines, a nuclear missile cannot be launched unless the two officers authorized to launch them physically insert and activate their launch keys simultaneously into keyholes that are physically too far apart for one person to do both. No computer hack can override that safeguard.