They had already won before the final, that much is clear, but I can't for the life of me understand why they didn't just put up a proper fight in the final. It didn't matter who won the last fight and it would be fun for all involved to have a good scrap.
If I were CCP, I would seriously consider some form of punishment. This isn't supposed to happen in sports - which the AT9 definitely is, with fans, viewers, sponsors and all. Deciding on the right thing to do however isn't quite that easy.
Also, for the future, limiting the possibility of fielding multiple teams should be considered, but the problem with that is that it is pretty difficult to do without severely changing how teams are placed into the tournament.
Still, a lot of work went into the Hydra/Outbreak and it paid them with the prize of two final slots which is impressive.