Opening Tipoff went wrong way

[Roundball]

First time poster here. Wanted to ask about something I saw today on the opening tipoff of a Middle school game. Team 1 took the court and the jumper lined up facing the wrong way. Team 2 took the court and their jumper subsequently lined up facing the wrong hoop. Team 2 won the tip, tipping it forward and Team 2 went in for a layup. The referee signaled 2-0 Team 1 and gave the ball to Team 2 under the basket. Team 2 inbounded and scored right away and the referee signaled 4-0 Team 1. Team 2 coach called a timeout and pointed out the players were initially allowed to line up facing the wrong basket. The referee said it was not a correctable error and said its either 4-0 Team 1 or start the game over. The game was started over. If the officals allow the teams to go in the wrong direction to start shouldn't it be 4-0 Team2 and play resumed after the timeout call with the players going in the right direction (rule 5, section 1, article 3). Thank you.