You don't exactly need to base your skill on points. You can do it on kills, by subtracting how many points they've gotten from caps. If you have more kills, you know you did better than them.
I would support separating the two point scoring ways, though--one column for flag caps, one for kills. It's a bit annoying to subtract, and the fact is, the two really aren't the same. It's easier to capture the flag than get 25 kills anyway.