Rather than rewarding sheer volume, or having a net win/loss score based on often uneven match-ups, how about a system based on the rating points won/lost by each member of the clan in the games featured in that challenge?
e.g. (for a one v one challenge)
Player x picks up 15 rating points for beating and drawing with player y.
Player x's clan gets +15 pts, y's gets -15.
You could of course have this on top of the more conventional ways of ranking clans.