The Gabonese striker repeatedly saw his future called into question in his final half-season at the Westfalenstadion, before finally departing on deadline day last week.
Gundogan, a former teammate of Aubameyang's at BVB, believes that the public spectacle possibly hindered the Bundesliga outfit as their results dropped during the striker's time out of the side.
"I don't know if I could have done it like Auba did," Gundogan, who quit Dortmund for Man City in 2016, told Sport Bild. "At that time I was also criticised for my open change intentions at BVB.
"The reaction of the fans I understood a bit. But I only wanted to be honest and always gave everything for the club. Both parties live with the solution taken, although Dortmund loses a very, very good player. I very much hope that now peace is restored. Because you need it to be successful in the Bundesliga.
"All the bickering was certainly not conducive for the performance of the team. As a player you get on with it, and if you read any negative things in the paper every day, then it's a burden. That's a hindrance to getting full performance. I keep my fingers crossed for BVB that the club qualify for the Champions League. It would be nice if I see the boys there again next season."
Aubameyang marked his Arsenal debut with the fourth goal in their 5-1 win against Everton last weekend.