I would make it so that Forts no longer gave points every 10 minutes or whatever it is currently. Instead, make it so that all the points are accrued during the Fort siege window. Meaning if the faction wants to gain points from said fort they'll need to actively hold the fort to accrue maximum points during the siege window. Basically a king of the hill scenario.
Example: 2 hour siege window
Faction A holds fort for 25 minutes 1,250 points
Faction B holds fort for 70 minutes- 3,500 points
Faction C holds for for 25 minutes 1,250 points
I would develop the fort siege system even further by having small points of interest in the vicinity of the fort that could be captured at lower value to generate points as opposed to just one circle.