You're on the right track Pseudo. Heres what I did. I had a func_capturezone tied to the main CP. When capped, I had a relay temporarily enable a trigger_capture area which capped an invisible CP like you suggested. Worked fine on the test CP. However, when I multiplied that for all 5 CPs, TF2 started crashing. I believe there is a limit of 8 CPs in the game. FYI.
So the final solution I came up with is having the trigger_capture_area tied directly to the main CPs (no invisible ones). So a flag carrier walks into the func_capturezone, which triggers a relay that temporaily enables the trigger_capturearea (set to a 0.01 second capture) which then captures the CP. Phew! Seems to work 95% of the time, but I have yet to test it in gameplay. One drawback I already see is that any other teammate standing on the CP will get credit for the cap too. But I can live with that.
So this solved my dillema with crediting people for capping CPs in an Attack/Defend style map. I still need to figure out how to give points for destroying the enemy control room.