I'd like to start by recommending that people read the "How to play CTF" sticky since it has some good information about CTF roles and strategies.
As "How to play CTF" points out attackers tend to end up with higher scores than defenders since they get 20 points per flag capture. What if the scoring system were changed a bit to better represent the contribution of defenders to the team.
One approach is to award additional frags when an enemy is fragged within a certain radius of the flag. Another is to award additional points to players that frag enemies who have flag even if they aren't the player to return the flag.
Part of what I'm assuming is that ideally the scoring system is calibrated so that each player's score is reflective of his contribution to his team; and maybe that's controversial. It's a tricky goal since changing the scoring system may change what the ideal behavior is that is to be rewarded.