This is a neat premise. I'm thinking something like awarding "x points" per "y time" you are in a cap zone. And a fixed reward for being in a zone at the end (like we have now). Since we already do have a score multiplier for capping a zone with other players, this seems like a logical addition.
For instance, you are the 1st into a zone, and stay there for 20 seconds (the cap is available, but at a stalemate, 2 pts/10sec) and you kill 3 people, and then the cap commences, and eventually gets captured. When it gets capped, you could get a score like this:
3 kills x 4 cap help pts + 10 cap = 12 pts
Perhaps, even this case could happen:
0 kills x 0 cap help pts + 10 cap pts & no assist points = 10 points.
Thoughts?
(seems like a cool idea for a teamwork mutator)