Goals from home debutant Gedo, within 90 seconds of his half-time introduction, and Ahmed Elmohamady were enough to secure the win over the visitors, who had levelled on 84 minutes through Jamie Ward only to concede soon after.
"It would have been a thoroughly deserved point. It was a very good away performance at one of the favourites for promotion and I can't ask any more from our players whatsoever," he said.
Clough said he felt there was a handball in the build-up to Hull's winner, adding: "That's two major decisions in four days that have gone against us."
Gareth Roberts was shown a late red card for a high tackle on Nick Proschwitz and Clough said the Rams would not appeal the decision.
"He's gone for the ball definitely, but with the ball being off the ground he has to be off the ground as well.
"We don't usually appeal these things unless it's blatantly obvious, so I don't think we will be, but it certainly wasn't intentional."