What about this:
If a player kills a guy from his own faction he gets a "bounty" point and loses some rep. The kill is counted not by the final blow but by the amount of damage dealt before death, so if a guy is lasthitted by some monster but you did the most damage before that, you get the kill. The "bounty" points have a timer of 3-7 days, the faction has a short memory. When a player accumulates 3 points he becomes "marked". Once the "bounty" points drop below 3, the "mark" status is deleted. The "mark" can be seen with awarness. If you kill a "marked" player you don't lose rep. Once the killer has 3 points, any player from his faction can go to the "Bounty Hunter" NPC and open a request for his head, the player that opens it pays his own money as bounty. If the "marked" killer stays hidden long enough that his "bounty" points are forgotten, the bounty request is deleted and the money is returned to the opener. If the "marked" player is killed by another guy from his faction,let's say "hunter", the "hunter" is the player that dealt the most damage before the marked target died. The "hunter" has the ability to use an axe on the "killer" body and chop his head off, yes you will need to carry an axe. The head has a life timer or 24 hours, after that it becomes rotten and unusable, the head can be sold to the killer for caps or gear. The head has the name of his owner on it
. Once the "hunter" has the head, he can hand it over to the bounty hunter NPC, the "hunter" gets the bounty assigned for him, and the "killer" gets -10k rep for each "bounty" point that is active at that moment. The points are deleted after that, so he is 3 kill away from being "marked" again. The person that opened the request, gets the head for his money. He can put it on a stick in his room or platoon base.
Regarding the patrols, best way is see it is to tie them to assignments. Stay near NPC patrol for xxx minutes, get caps and exp. Easy patrols at the gate, hard patrols deeper into the city. The patrols can be done only on maps owned by the faction(gate+ZC). So if you have no zones, you can only patrol the gate.