Just some off the wall ideas. Sorry if I"m a bit all over the place, have a head cold. I"m sure more experienced pvp'ers could easily come up with better ways to implement these.
Make a specialized faction claim block that gets perks by being purchased from trader joel. Such as increased land claim distance, tougher defenses, energy gird, bonuses to mined ores within the radius, bonuses for players mining, attacking, etc. The list can go on and on. Make the fight be over the faction claim block. Destroying it gives the winning factiona set number of duke coins. This will be based on the raided factions claim block rank that they purchased. Having their block destroyed reduces the raided teams benefits that were purchased from the trader. Allow players to sell back benefits in order to purhase different benefits. Once the faction block is destroyed it ghost making it impossible to hit. Also allow the claim block to open like a chest where its stores the players bed rolls. They have to remove their own bed roll in order to stop spawning there. Once the claim block is ghosted, that faction is auto flipped to pvp passive mode and their base becomes 100% indestructible. Either until a cool down is reached or a visit to trader Joel to pay to have it flipped back on immediately.
A faction block, once placed, can't be moved without losing all the current perks. This prevents factions from needlessly move their claim block around. Designated team leaders would also be the only ones able to move the block.
Trader Joels insurance on equipment. Allow players to purchase insurance to attach to their equipment. If a player is killed via pvp, only items on them that can be looted are those without insurance. The killing player instead recieves a set number of duke coins in place of insured items. The respawned player must reinsure his items again in order to recieve the item protection. If the player is killed and belongs to a faction, he respawns at his bases faction block. IF he is a new player who flipped his pvp flag, he is sent back to his bed roll. If a bed roll doesn't exist he is respawned at the nearest trader joel. If he was flipped to pvp when he died, then his bag is lootable.
New players joining the server who don't belong to a faction will have the pvp flag off by default. In order for them to be able to attack any one, they would have to flip their pvp on in order to engage in pvp prior to joining a faction. If its on and the a player rolls their cursor over the other player they recieve a warning that the new player is in pvp mode. Also, when the player flips to pvp mode, have it make a lound noise. This warns other players an attack is imminent. This will prevent a new player from just walking up and flipping to pvp next to a player in faction mode. Past that, they would be under friendly fire off mode unable to do any damage to players or buildings that have a faction claim block.
Also, maybe a system that warns new players that they have entered a pvp claim area and put them on a set timer. If they stay too long, they can be shot. This prevents them from waltzing around players bases in order to shout out locations, orders, or to come up with a plan of attack.
Also, if you don't belong to a clan/have a claim block you can't place any objects down in the protected areas x amount of spaces from a faction claim block.
Players who don't belong to a faction can place a bed roll anywhere outside of claimed areas.