Back then, was there already a 'master plan' by the writing team that Cardassia under Dukat would actually be joining the Dominion 1.5 years later on?
I think almost none, and any plans they did make were totally ineffective. From what I've read from various sources, Behr et al hoped to get to the war by season 5, probably wrapping it up that season. However, the interests of the studio conspired to push the war into the future, and their own inexperience with writing with this level of continuity meant that even plans they made in the short term had to be rethought on the fly.
The Klingon-Cardassian War was itself something they had not planned for, necessitated by studio interests, particularly the introduction with Worf. Behr has described most of season 4's developments as largely a distraction. Because of what happened, it may have seemed as if Dukat was being redeemed, something which Behr never intended. Given that, I think that Dukat's selling out to the Dominion was likely something that was done because it would be so dramatic.
Something else that seems to have been intended was that the war would be wrapped up several episodes into season 6. Initially they were given 4 episodes to do so, but found that they best they could do was recapture the station in 6. After that, they had to "pay the bills," so to speak, by producing episodes that were more like stand-alones, wherein the war was more of a backdrop.
Did they want a war? Yes.
Did they want the values of the Federation to be internally tested? Yes.
Did they want Klingons to join? Possibly.
Did they want Dukat to betray them? Probably not.
Did they envision a role for a secret organization? Probably not.
Did they want the station occupied? Unclear.
Did they want Sisko to conspire with Garak to bring in the Romulans? No.
Did they want Sisko to peel potatoes in his father's restaurant? No.
Did they want Damar to become a revolutionary? No.
Did they want Sisko to become a Prophet? Most likely yes.