As a member of a guild that has made the climb to b6, I can attest to the frustration accompanied by month after month of fighting dead guilds.
I am not in favor of punishing the guilds that have earned their place at the top. To me, it is as simple as this: There is a system already in place for advancing in Rank for Bracket winners. Use the same method in reverse for the losers.
The guilds that field 3 players will soon disappear from competition.