I don't think that will work. 3 sides (a triangle, if you will) is self-supporting. Generally it's more stable than 2 sides. With 2 sides things can collapse much faster, especially if sides go unbalanced.
Hrm... maybe a perk multiplier incentive? If rooks have 120 players, knights have 60 players, and bish have 70 players, then bish and knit get a higher perk multiplier for ROOK KILLS. They get standard multiplier for knit/bish kills.
That would add incentive to even things out, right? EDIT: I mean, the bish and knit would both be inclined to attack the rooks, and it would help lessen the strength of the rooks to fight on 2 fronts. Sort of like an unofficial alliance, created by perks.