1) Cool concept
2) So that the player doesn't get annoyed: "It is VERY IMPORTANT that you don't set the operation to auto-complete until you complete the first stage. If you set it to auto-complete then it will skip over the choice and choose for you, which kind of ruins the point."
You just need to split the two operations into five:
Sabotage Weapons - Kinetic
Sabotage Weapons - Energy
Sabotage Weapons - Explosive
Sabotage Defenses - Armor
Sabotage Defenses - Shields
3) Even if you didn't like point 2, you can still add a third function to "Sabotage Defenses":
Sabotage Defenses - Hull