Was playing a Siege last night and unfortunately us attackers were seriously underpopulated (I know balancing is something that is already been discussed). That said, we still managed to get a good number of soldiers into one of the caps and we were almost able to take it when a respawn wave happened right in among us! Suddenly the small handful of us were outnumbered and quickly cut down.
If a cap area is contested, I think respawns at that cap should be halted until such time as that cap is re-secured by the forces already there.
In a situation where it is the last cap - I would suggest instead having the respawn moved to a "relief force" respawn area outside the defensive structure where the defenders will have to push in and try to regain the balance.