Oh there are some answers without "ruining" Eve.
Example; CONCORD declares the CFC a terrorist organization, and affiliation with them automatically grants criminal status. They get locked out of high-sec, and even low-sec services, are shoot-on-sight to all navies, and blockade posts are set up on the access jumps into CFC controlled null-sec. Now, should CONCORD and the four empires go charging off into Null-sec and start wasting Capsuleers? No, probably not. But good luck getting through High-sec without the local system defense fleet showing up.
I don't see CCP doing that. Much as it would help curb their general "fuck everyone else" attitude and as much as it makes sense in-universe, I don't think that CCP as a corporation cares. If they want something to happen, it'll happen anyway. It'll just get written in as lore. And as cool as the lore is, just reading about events is really dull. Compared to, say, participating in events.
"But Kane..." I hear the reply, "There -are- events players can participate in! Player events! Null-sec stories and arcs! The glorious battle for freedom, resources, ISK and PLEX!"
But not everyone is interested in the null-sec content. Just like in WoW, not everyone is interested in end-game raiding, or the PvP arenas. WoW at least had some diversity, in the PvP/Normal/RP servers; you could kind of pick and choose where your focus was. But Eve wouldn't be able to support that model. Or, possibly it could. It'd be interesting to see how they might handle something like that, just from a theorycrafting standpoint. But I'm getting off-topic.
The point is, the RP community, those interested in the live events, can't beat the Goons. Partially because they have different victory conditions than everyone else. Part is that they have more resources than God. Part is that the line between game and meta-game is very thin (or non-existant). And part of it, as mentioned, is that if someone really wants to kill you badly enough, there isn't a damn thing you can feasibly do to stop them.
And, to reiterate the first solution I mentioned... I'll point out that firing on any actual military vessel will get you declared as an enemy combatant, and probably be viewed as an act of war. Given CFC's behavior in-game...