Two possiblities:
Make the available shadowbreed for a player based upon their SL faction, not their RK faction.
Make both shadowbreeds available to clan and omni of the same breed, but have them share a lockout.
Potential issues:
Removes a unique ability of being clan or omni.
Shadowbreeds being changed like this would have greatest impact on PVP, arguably affecting a key part of PVE content.
People would no longer have shadowbreeds to blame for losing.