Yeah, I always call the merchant before disputing. 99% of the time they'll refund the charge right away.
Not sure about 99%, but it's the right thing to do.
The only dispute I had on my direct CC merchant was from the rabbi of my shul, he thought I over charged him so he just disputed. When I comforted him he said "you should have told me then regarding the charge" I said I did and even told him where he was standing as I told him in person. He denied that but after reviewing the cheshbon he reversed the dispute.
I was more hurt from the fact he wasn't a mench and just ask me before he disputed, at that point it bothered me more then the money involved.
Lesson learned, I do everything over the phone on a recorded line