It had looked like the west Londoners would secure the three points after seeing debutant Bobby Zamora break the deadlock in a first half they dominated.
The England international's fledgling partnership with Cisse looked promising, but it only lasted 34 minutes after the latter was sent off for retaliating to a Roger Johnson challenge.
Wolves went on to win 2-1 thanks to goals from Matt Jarvis and Kevin Doyle and, while frustrated with the result, Hughes was keen to focus on the positives after the game.
"I was really pleased with what we were producing," the Hoops manager said. "I thought the interplay between Bobby, Adel [Taarabt] and Djibril was excellent.
"That bodes well for the future and that is a real positive from my point of view.
"Obviously we are disappointed today [Saturday] because we have lost a key game, but I think moving forward we now have real options up front.
"Djibril will be missing for a number of games but I thought Adel coming back really helped us.
"If we had 11 v 11 I feel very confident in saying we would have won the game quite comfortably.
"But unfortunately we weren't able to keep 11 on the pitch and we conceded two poor goals in terms of what we could have done prior to the goals going in.
"I felt we did really well defensively but then we let ourselves down somewhat, certainly for the first goal and maybe we needed to be a bit stronger in our challenges for the second one.
"At 2-1 down and one less guy on the pitch, it was always going to be a tough task for us.
"But I thought towards the end we really took the game to them, had some great efforts and on a better day for us we might have converted one.
"It wasn't to be but, as I said, I was encouraged by the performances of a number of players today [Saturday] and we will be better for that."
Hughes revealed Cisse apologised to his team-mates after the match and can understand his reaction given his history with long-term injuries.
"I think obviously we were disappointed with the initial challenge and given Djibril's playing history and the injuries that he's had, he reacted to that," Hughes said.
"I think if he had just kept it at the initial reaction when he jumped up and confronted the guy, I think he would have been all right.
"But then he went back again and raised his hands to the boy's neck area.
"As we all know, you can't do that and the referee, unfortunately from our point of view, had to send him off."
Wolves counterpart Mick McCarthy struck a relieved figure after the victory, which came after a nine-game winless streak.
The three points propelled his team out of the relegation zone and comes after a 3-0 home defeat to Liverpool.
"I've been under pressure for the last 20 games as I've only won two of them," he said.
"I was under no more pressure from Wednesday night than I've been for the last 20 games."
On Cisse's red card, he added: "You know me and my sentiments towards football now.
"That for me wasn't a sending off when I played and, strangely enough, Roger's tackle wouldn't have been a booking.
"But it is and the sending off is because you can't grab anybody by the face because it's not allowed any more.
"He was playing well so he's made a mistake and cost his team. And it did because the extra man paid dividends.
"I don't regard myself as unlucky but we weren't having too much of the good luck so one man's mistake has given us the opportunity to win a game."
McCarthy revealed after the match that on-loan Arsenal midfielder Emmanuel Frimpong will have a scan after coming off with a suspected knee ligament problem.
"He's got a brace on and he was carried off," he added. "On a scale of one to 10 I have got no idea. I haven't got a clue."