If self defence wasn't a crime then if you shot someone first and they shot back in defence, your computer would not recognise it as a crime and therefore not report it...
If both players are clean and have crimes on, in your scenario, the aggressor becomes "wanted". All is well. The disconnect is this artificial "crimes on/off" flag for game reasons. Self defense becomes a crime when the victim in your scenario has crimes turned off. Its as if he's flying around in his own little anarchy bubble. That's a self imposed disadvantage in the current system.