The Football Association have charged the Manchester City striker with violent conduct after he struck former team-mate Robin van Persie in the face with his boot, as well as for misconduct after he ran the length of the field to celebrate in front of the visiting Arsenal fans following his goal in Saturday's 4-2 win over the Gunners..
"My thought is that Emmanuel Adebayor deserves to be charged for what he did," said Wenger.
"But I was surprised that there was such animosity in his attitude towards Arsenal because in a few years he will realise that Arsenal has been great for him.
"That is why I was deeply surprised and shocked."
The Gunners boss continued: "Only he can say if he will regret leaving.
"All I can say is that is life and professional football players move on.
"In life, the goal is to be objective enough in seeing who helped you and who didn't help you, who had a positive influence on you or not.
"You can sometimes be disappointed in the short term. But still I believe that when you take distance with the events, you always get to the right judgement.
"I think the longer distance will make Adebayor realise that Arsenal was a very positive influence in his life."