Avoiding another Eager situation in SMITE

This morning /r/smite and Twitter were abuzz with details of the Eager drama. ATR's side, Zapman's side, players speaking out... why did this happen? More importantly, how can we prevent it from happening again?

Should SMITE’s tournament structure be changed?

Your favorite team. You've been rooting for them all season long. When the big tournament rolls around -- say, SMITE's recent Spring Masters event -- they play one best of three and... that's it. They lost. They're out of the tournament. Is this good tournament design?