One of the plugins I've seen that did a pretty great job of not just creating limitations for groups working together, or access on locked things, but actually works to cut back on people swapping out teammates or working in multiple smaller groups to bypass limitations came from the Plagued plugin.  From that page:

 

Features

  • Automatic associates detection and penalty attributions.
  • Radius based proximity detection
  • Incremental penalties
  • Time based progression and recovery
  • Kin system (Teams)
  • Commands
  • Configuration files
  • Database persistence

Usage

When you get close to a player, you start building up affinity. When you are far away from that player you start loosing affinity, but much slower. This is so you can still collaborate with other players without any penalty. After several minutes of proximity either continuous or briefly interrupted, you become associated with the player with which you have been playing. At that point, you start gaining plague levels. The higher the plague levels, the higher the effects and it takes ten times longer to heal that to get sick. Also, the rapidity of the onset and severity of the symptoms depend on the amount of associates that you have.

It still has to be fine tuned, but the idea is you can still interact with your neighbors, or group up for a multi-crew raid, but you can't live in close proximity. At default levels it takes eight continuous minutes to become associated and fifteen continuous minutes to reach the maximum plague effects. Inversely, it takes 80 minutes to reach zero affinity and 150 minutes to lose all plague effects.

Plague Levels

  • 1 - Decreased Health Regen
  • 2 - Increased hunger
  • 3 - Increased thirst
  • 4 - No Health Regen
  • 5 - No comfort
  • 6 - Highly Increased Hunger
  • 7 - Highly Increased Thirst
  • 8 - Cold temperature
  • 9 - Bleeding
  • 10 - Poison effect
One of the best parts of the system is that you have to pick who you're immune to early on in the wipe, and depending on the configuration settings, that can't be changed until a map wipe.  The time for infection and healing can be controlled too, making it possible so that anything other than just quick trading can drive the affinity rate way, way up, and then straight off into debuffs or even damage, and a prohibitively long time to recover.  Add something like auto-locking containers, and one team farming for another team to raid is pretty significantly hampered.