Basically: under the current "scoreboard" system, I can't tell my NPCs not to shoot my friend unless he's in my team. What I want is a few levels of relationship:
-War
-Peace (the default)
-Non-aggression pact (can't attack for 7 real-life days, option to autorenew)
-Guarantee Independence (one-way mutual defense pact)
-Mutual defense pact (each side defends the other if attacked)
-Military Alliance (each side joins the other's wars, even aggressive wars)

Additionally, you might have an option to set your relation to war by default (in a normal factions server, for example). You might also share some claimed things, like gates, so allies can for example set up a courier route to bring trade goods.