Suggestion 1:
In lack of players we still have 10-20 from V-tech ready to do ZC. But no one else comes.
To solve this problem without changing the faction system, it would be cool to give ability fight inside the faction, getting score.
Group of player comes to the flag, everyone tagged the leader. Leader takes the flag and group temporarily becomes hostile to all other players from the same faction. If capturing or defending group from same faction wins, zone stays for the same faction, in any other case standard ZC rules applied. Reputation for such ZC is not required. Event still open and anyone can come to fight the group, so it shouldn't be much easier exploitable than usual ZC.
Suggestion 2:
To prevent multi-zone capturing it's possible to deny right of a character to be counted as legit to start zone control if he has been in the zone during initiating zone control which is not ended.