Nathan Blake was Wolves' matchwinner with his first hat-trick for the club as Dave Jones' men secured their third successive league win.
However Blake angered Gills fans by being carried off on a stretcher in the first half only to return and condemning their side to the heaviest defeat of the season so far.
Blake who scored in the corresponding game last season which Wolves won 3-2, was involved in the night's most controversial incident midway through the first half. He raced into the box before being brought down by Nayron Nosworthy which earned the Gillingham defender an immediate red card.
Blake meanwhile was receiving treatment and was then carried off by first aid men and received more attention on the touchline, before hobbling to the dug-out and then going back on.
Collin Cameron converted the spot-kick but Blake then popped up with Wolves' second on the stroke of half time However the real damage was done in the second half as he completed his treble in the space of seven minutes. Cameron set up the second with a cross to the far post which Blake converted and then the 30-year-old Welsh international added his third with a fine individual effort, sending a low shot past fellow Welshman Jason Brown.
He had a fourth ruled out for off side before Wolves hit the bar with another effort from Kenny Miller.
Gillingham kept battling away despite being a man short but created very little to worry Wolves keeper Matt Murray.
Earlier Murray and his defenders were under pressure early on as Gillingham tore into Wolves at the start.
However Wolves stood firm and were almost gifted the lead themselves. Brown rolled the ball out, only for Blake to react quickest and it needed the Gills keeper to save his own embarrassment by blocking the effort for a corner.
Referee Matt Messias who once sent off two players in an earlier visit to Priestfield struggled to keep control particularly in the first half, apart from Guy Ipoua for delaying the penalty, Blake and player-manager Andy Hessenthaler were also yellow-carded for a first-half spat, then in the second half Wolves had Kevin Cooper and Marc Edworthy booked for fouls.
Hessenthaler refused afterwards to criticise the referee adding: "I am disappointed with the result and it was probably a penalty but to show Nayron a red card with so many bodies around was a decision that the referee had to make." Meanwhile Wolves boss Dave Jones said: "It was a clear penalty to me. Nathan was abused by most of the crowed, but you only had to see his foot in the dressing room to know that he played on with a nasty injury."