Yup, Dukat definitely considered Sisko to be a friend. Sisko was kind of a prick about it and didn't return his friendship, though. You'll find out better when you get to the episode "Waltz" which is an amazing episode that explores the Dukat/Sisko relationship. However, Waltz had a different ending originally than the one they ended up putting in the episode. The ending they chose to go with was a really bad decision. Unfortunately it pretty much sabotages the integrity of the Dukat character, which is almost universally regarded as the biggest & most-hated fubar of the series. But you'll understand that better after you've seen the whole series.
What was the original ending?
thanks,
CDP