Limiting the clan size would never work for all the good (and some bad) reasons mentioned before.
Having clans join one of the "Kingdoms" - think Swadia, Vaegir, and Saracen - having official meta-clans, would probably be a better way. You can ONLY sign up for battles with your kingdom OR for either of the opposing kingdoms when they fight. In other words, never against your own Kingdom.
And factions could only accept clans or characters so long as it didn't push them beyond 20% the size of the smallest ingdom. OR impose an incentive for joining smaller Kingdoms, such as a significant XP bonus for joining and fighting for the underdog kingdom in both cRPG and Strategus (active so long as you participate in Strategus battles to ensure actual play).
This gives new players and lone wolves some safe haven, automatic allies.
Rules for in-fighting might even be put in place - as is historically accurate and fun. Can only be done with sufficiently high renown for example.
I could go on an on fleshing the nuances of how this would work, avoiding loopholes, etc. but ahhh well.