It would still be attacked, only the local system security would then be fighting with you and your FC security. You see a FC drops into a system and starts launching hostile ships, what exactly do you expect local security to do? Nothing?
This is an odd reply. You seem to be pretending, in your reply, that there are actual people flying actual ships and giving order to people who fly ships. "zomg go attack that carrier" - you imagine them to say.
But there are no actual people. It's a game. And the presence of the ships is a game mechanic. The developers can make it anything they want, and then explain it any way they want.
So no, it's not true that "it would still be attacked" if my suggestion was implemented.
But just to run with your hypothetical (where we imagine there are actual people commanding the system security) - how do you explain the situation where two minor factions go to war, and afterwards one of them controls the system, and the other one controls a tiny outpost (an outpost smaller than an FC)? How do you explain the fact that the controlling faction doesn't attack the outpost?
Whatever answer you have - please apply the same logic to my FC.