Frag should be counted without doubt. CTF team works together, important frag can decide whole game etc. Everyone has different function, defender kills attackers and returns flags mainly, he is not able to carry many flags. He deserves to be rated as well.
1 frag = 1 point
killed flag carrier = 3 points
flag returned = 1 point
grab opponents flag from base = 3 points
grab dropped flag = 1 point
flag scoring = 5 points
there would be the possiblity to drop the flag, indenpendce on rockets if your health is 5% is not too suitable :-) I would like to see team damage in the future, because spaming :-) and it brings different way.
What about to divide a map into more parts. If you kill flag carrier in his base, you should get more points, because it is harder than in your base etc. Mathematic distance from your base etc.
What about to do this: during final screen after CTF battle to show: Rambo of the game (the best killer), the best teammate (most points except of frags), and MVP - most valuable player (all points overal).