Here is my easy solution (stolen from many others bright ideas already on here) for Crpytic,
You have the entire universe in instances. Just make a mirror "Open PvP" instance. Space only to start since that is what is good about this game. Add ground later. Fed players who want to do a mission in the "Open PvP" instance get to click on it and bang they are playing the same instance they normally would with the addition of possible Klingon live players. That particular Klingon is dead when you kill them, they can't come back (or give them a really really long spawn timer). Your a fed so we will let you re-spawn.
Klinks can put themselves in the "live open PvP" queue and when feds wants one: bang we are there.
Heck we might not even show up right away. But your doing your little mission with the "fear" of a live Klingon player out there. Add rewards for killing live Klingons in addition to regular rewards.
To test this just use Fleet actions only, and allow Klingon's to spawn in based on Fed population at present. Once your in as a klingon, your in till you die. We get boasting rights(and exp and medals) for how many waves of fed respawn we can kill...lol
Feds still complete mission eventually since once the Klingon's die they are dead. Everyone wins. Would be a hell of a fight, and makes your missions way more fun for hardcore feds bored out of their skulls. And if you have a ear to your game this is your biggest problem going forward. You simply will not be able to make enough content to keep people happy. This gives us all something to do, and its easy for you to implement.
Oh and make sure you have different spawn points for both factions if you do this. (OB live event?? remember that?)