Gareth McAuley's own-goal gave United the lead but Robin van Persie had to climb off the bench to seal the leaders' win in the last minute.
"It is not demoralising," said Clarke of Van Persie's introduction.
"The fact they had to bring some of their big guns off the bench shows how well we were doing.
"In the first we were too timid. We spoke at half-time about being too respectful and in the end, the scoreline doesn't reflect the way we played."
Clarke rejected suggestions the pitch, which needed to survive an inspection for the game to go ahead, was too difficult.
"We used to play on pitches like that all the time," he said.
"It is part and parcel of the game. You don't look for games to be called off for no reason and there was no reason."