You can use a combination of keys which are bound/unbound, via warcrafts keybindings. Anything you change here for a given account will remain no matter which account you are driving.

You can also add either Do Not Pass blacklist (these keys are not broadcast) or Do Not Pass whitelist (only these keys are broadcast) within Keyclone. In this way, you can control your main with WASD+QE, no matter who your main is at any time, but not have the followers use these keys.

It would be neat, but I don't think you can do this yet. Have the opposite, keys which are broadcast to the slaves that you are not on, but which don't do anything for the toon you're currently controling. Kind of like a reverse black list, which does not apply to the current main, only the slave/followers.