Hughes departed his role as Easter Road manager last month after Hibs won only one of their first 10 games this season.
Hughes had persuaded Stokes to move to Easter Road from Sunderland on the back of their successful spell together at Falkirk, and was rewarded with 22 goals last season before the striker's move to Celtic earned the club more than £1million.
Hughes told BBC Scotland: "My biggest disappointment and a wee bit of frustration (was that) seven games into the season you lose the top goalscorer and then four games after that you're out the door.
"I will take it on the chin and get on with it, that's open to the supporters' and pundits' interpretation of it.
"I just felt a wee bit let down, losing your goalscorer seven games into the season and looking at those seven games in more depth, knowing the plans that were going on at the club and never getting the opportunity to follow them through."
Hughes added: "If I knew four games after we let (Stokes) go to Celtic that I would be out of a job, I would have fought harder to keep him.
"I thought there might be a bit in the club to understand, batten down the hatches, we're losing 22 goals."
Hughes was believed to have been planning major changes in the squad next summer with 16 players out of contract.
But Colin Calderwood now has the task of rebuilding the club, and Hughes has urged the Hibs board to give his successor time.
"I'm 100% behind Colin Calderwood," Hughes said.
"I'm banging the drum right now - give that guy three or four years. Let him get his own men in, get his own players in and do it his way.
"Football in Scotland is a fickle business, everybody needs time.”