Puppeting wouldn't test the skill of the better player, merely the willingness of the less good player to to follow orders. Is it will be the same as if a top player just used an alt.
I always thought a really nice game to do would be no communication at all between the teammates. A very good team could work on instinct if they have played together a lot. This would properly test the skill of the team rather than the better player in the team.
Obviously you would need to trust people not to just chat via some other form of communication.
Anonymous accounts and a block on team chat could do the trick.