Flower became the first man to be sent off in a Super League Grand Final when he knocked St Helens' Lance Hohaia out with a punch before striking him again while the half-back was motionless on the ground.
The 26-year-old Wales international has since been found guilty of a Grade F offence by the RFL and banned for six months, which equates to 13 matches overall.
"I'm not surprised. It was a pretty unsavoury incident," Wellens told BBC Radio 5 live.
"He's come out and said it himself that he's very disappointed with his actions. It's quite clear the RFL has sent a message - that type of behaviour won't be tolerated."
The ban is the second heaviest of the Super League era, although Wellens is confident that Flower will be "treated as normal" on his return to the game.
"Rugby league people in general are quite forgiving. There'll be a lot of scrutiny around him when he returns as a player," he added.
"But within rugby league there's been incidents in the past and people have come back. He'll be treated as normal.
"He'll go away and serve his punishment and then once he's done that I think he should be allowed back in and straight back into the Wigan squad as per normal."
The Saints went on to win the Grand Final 14-6 at Old Trafford.