You can easily put your clan in one team and the rest of the players in the other team (and keep it that way).
Tested with Counter-Strike 1.4.

We've had a lot of fun on our server with this. Imagine: cs_assault, your clan vs the rest: 3 vs 10 :D

Commands:
admin_war <ct|t> <clantag>: Puts a clan in one team, locks the teams and restarts the map.
admin_war_ct <target>: Like admin_ct, but this one should be used instead during a public clan war.
admin_war_t <target>: Like admin_t, but this one should be used instead during a public clan war.
admin_war_stop: Ends a public clan war.

IMPORTANT notes:
- The maximum possible amount of players during a war is 10 per team. If the team of the opponents is full (10 or more), a password is set on the server. You can edit that password in the script.
- The Admin Mod access level of ordinary players is set to 0 during a war.
- Players are well informed about a possible war going on: in the console as they connect, and when they are forced to join another team.