I'm not really sure how to call this one. Not much in the standard Smogon rules on ties. However, there is this.
Draws: If a battle ends in a draw in an elimination tournament or another tournament format that is unable to handle draws, there should be a rematch between the players with the option for both players to change teams.
With this in mind, I would recommend a rematch. If someone more knowledgeable, or perhaps authoritative, on the matter has some input on who should have won that, feel free to speak up.