Instead of making the ZC capture point an arbitrary flag, make it an NPC. Call him a Production Manager or something. Players from the ZC controlling faction can go and do menial quests in that area for xp, caps, and rep.
For another faction to start ZC, they have to execute the NPC. This could start a server message "Robco Production Manager has been executed." Then the faction that started the ZC gets "20 minutes until Production Manager arrives." At the end of the timer, whoever is in the lead spawns a new Production Manager with some nice reinforcements.
The NPC spawn could also prevent this whole, restarting ZC immediately after one team won.