United lost Flood in the 42nd minute after the on-loan Cardiff midfielder went down during a surging run, with Jackie McNamara in close proximity.
Flood had been booked nine minutes earlier following a late tackle on Jamie Smith and was duly shown a red card when referee Mike Tumilty decided the youngster had attempted to con him.
United recovered from that setback to snatch victory right at the death in the Clydesdale Bank Premier League clash through David Robertson's close-range strike, following a mistake from Andrew Considine.
Despite the late winner, Levein was still annoyed at Flood's dismissal, although he insisted he would not be blaming the referee for his decision.
Scottish Football Association chief executive Gordon Smith has vowed to rid the game of cheating.
And Levein said: "With all of the recent hype and publicity surrounding diving and cheating, there was an enormous amount of pressure on the referee, although I want to stress at the outset that I have absolutely no problem with people who dive or cheat being sent off.
"But it would have to be today for there to be a situation where the referee has a choice to make.
"And I knew with all the recent publicity that it was a certainty there was going to be a sending-off.
"Willo said he wasn't in the penalty area, played the ball past his opponent and was on for a shot at goal, so he had no reason to go down and he was just off balance.
"Sometimes there is a situation, such in the second half with Chris Clark and Christian Kalvenes, where it wasn't a foul or a dive and the referee got it spot-on.
"But I think there is now so much pressure on referees with all this hype and I don't blame him for a second.
"However, it left us with an uphill battle. Luckily we were fit enough to cope with it."