That being said, and on topic... I don't really see the place for this in the game unless they actually implement military/national security type organisations and the ability for the player to be employed by those agencies. It's certainly not the sort of thing that would be handed off as missions to non-affiliated personnel. And if you exclude missions and just do that stuff anyway then how do you quantify it's effect for the player?
It's exactly the sort of thing you would hand off to non-affiliated personnel, to create plausible deniability. Those carrying out the act may even believe that the stated objective is the real objective.
Since we're just talking about Elite here,

, let's say the Alliance Security Services want to distract the Federal Navies attention away from themselves for a while. Find some disgruntled Fed sympathising faction on an Imperial world, infiltrate and stoke them up to the point of sabotaging the Imperial Military. Cue interstellar incident.
When it all cools off, the Feds notice the Alliance navy has redeployed in an interesting fashion and says "hey wait a minute", reply is "What?, of course not, the very idea, pure coincidence, honest guv'" This denial is not plausible if the saboteur is an Alliance Officer, some smelly merc space trucker on the other hand. . .
Who carries out the sabotage, why not a PC? He thinks he is helping some local freedom fighters, but his pay, equipment and real objective ultimately comes from the Alliance. A bit strange in game as ad hoc missions but certainly a possible starting point for story arcs as Liqua mentioned.