If it were true that MOD were using civvies as mock target practise, then it would make an interesting court battle if an armed civvy (say a farmer, or offshore yachtsman) were to shoot back in self defence...
To convince the jury that you acted in self defence, you would have to persuade them that you were genuinely in fear for your safety. Even the most paranoid would have a hard time trying to prove that they believe an RAF aircraft on a training sortie in the UK would engage them with weapons!
Open and shut case. Take him down.