Like annoying mentioned there are some extra points already give for grabbing/carrying the flag. Schizazoid is also correct in that we can't be sure if score will motivate others to play more ctf. I'm sure there are some that are motivated by where they place on the scoreboard at the end of the game but I don't think it matters for everyone.
The biggest issue with changing the scoring system is that each change will affect the team balance. This is the main reason that flag killers are awarded somewhat highly for flag kills, it is an attempt to offset one team having a few dedicated campers which can create stalemate matches. This way the other team should get some stronger players who will hopefully be able to combat the strong defense somewhat. The balancer really needs a new feature to classify attackers and defenders so they can be distributed more evenly among the teams.