Logos,
Your suggestion would be fine as a means to keep the tournament running in the event someone has to leave. However...
I feel your suggestion isn't very inclusive. What this means is, the 5th player is just sitting on the sidelines, waiting on the offchance someone has to leave so they can play. Or they choose to swap him in, but then the replaced player can't play anymore. Remember, this is a video game; a MMO, we should have an option to allow as many people as possible to play with their friends, while keeping the tournament competitive. I feel 6 man teams strikes this balance.
I do understand your concern, but I noticed Blubbers updated the OP with new rules regarding player swapping. It would definitely keep things competetive by allowing the losing team to try a new composition, and this would keep the winning team on their toes, forcing them to adapt. All while still being inclusive.