I am totally sure of being accurate on this, but i feel that when you are in "contested" situation, the timer is totally blocked.
IMO, that timer should keep going. Not necessary by showing a timer (it can still show "contested" instead of it) but having all the faction actually keep getting points when the zone is contested. But no one would take the zone as long as the area is contested.
Takes situations :
- Faction A is taking zone. They need 10 minutes. After only 2 minutes, player X from faction B come up and hide. Faction A would still have to hunt him down and kill him/make sure he leaves. They shouldn't have the zone if there are still enemies around. But, let's say faction A takes 12 minutes to make him disapear, they shouldn't have have to wait another 8 minutes to have the zone. They stayed 10 minutes or more, and got rid of the competition. They did enough to earn the zone.
- Faction A is taking the zone. Faction B, C and D are all coming full force to fight them. It is a pretty tough battle that last one hour. At the end of the battle, only 2 members of faction D are still alive. They should get that zone, instead of having to wait 30 minutes with their inventory full of loot. They stayed enough to grab the points and they are the only ones left. They earned it.