First off.
Make it impossible for clans with less than, say, 10 members to declare ambush wars (formal allowed)
Secondly,
Add a player-count restriction to clan wars. Ie, any given clan cannot ambush another clan with more than 50 members than they themselves have. (Ie, WoD cant ambush Atreides because of the huge member difference. They would win easily and without opposition like this, since they can just kill all of Atreides lower levels and then sit back and wait for the timer. Boring.)
Thirdly,
Instead of only the clan declaring ambush gets a cooldown on their ambush against that particular clan, any clan who has been ambushed should get a cooldown on being ambushed equal to 3x ambush war time lasted.
And last
Make it possible to be at war with more than one clan at a time - ie, three clans can gang up (leaders send a 'gang-up on clan X request to each others by some feature) and, during the war, they will count as one huge clan for purposes of determining the fight, and during the war (ie, if clan Y has 50 members, clan M 40 and clan P 120, they would count for having a total of 210 members and would be able to ambush their enemy clan, X, if they have within 160 and 260 members only). The fight would then commence as normal. This makes it more attractive to have 'allies' as a clan.