But a fighting second-half period saw skipper Julien Baudet and striker Tom Pope reduce the arrears.
Thordarson was unhappy with Stockport-based referee Scott Mathieson and his female assistant.
"It is clear Billy (Jones) was grabbed by the player (Robert Snodgrass) first and he was then sent off for abuse of language," said Thordarson.
"Obviously we need to be cool and calm in our approach, but that was not an acceptable decision. Why was the female linesman moved away from the line by the Leeds supporters for the second half? If she was not capable of coping why was she put on the game in the first place.
"They knew it was going to be a tough game, Leeds are fighting for promotion and we are fighting for our lives. We can't have some experiments taking place.
"I was very proud of my team and my players. We conceded some soft goals, but responded in a positive manner and while we lost a game of football, we were the winners today."