The advantage is only a problem if you look at it as an 'advantage'. It really is just a team needs to lose twice to be knocked out of the tournament. Ronin lost twice. Froyotech lost once.
Its just like having a bo3 game again, but just in case the underdog team wins, then they can play the second game immediately after. If the second bo3 had been scheduled for the following night and then Ronin won the first map again and Froyo the next two, I doubt you would even raise an issue since you wouldn't be looking at it as "Ronin won 3 maps, Froyo won 2 maps"