I obviously don't know what the producers had in mind, and I'm guessing I disagree with Ron Moore on the impact of his work. However, here is my answer.
I disagree that Roslin and Adama are the joker and the thief. I don't think taking the song quite that literally is a wise move, given the subtle implications written into the tv show. I believe the cylons combined with various humans at various moments represent "the joker and the thief". This makes more sense than assigning two specific individuals to the roles of joker and thief, as even in the song, recall, the joker and the thief are not specific characters so much as stand-ins for every outcast turned revolutionary.
I believe that the show eventually transcended notions of good and evil as embodied in the human v.s. cylon battle. I think this is the root of the show's brilliance. The cylons were created by humans, and were themselves the result of previous incarnations of cylons on previous worlds. The show, I think, hinted that this is inevitable--that cylons are the height of hubris and the result of fundamental human misunderstandings regarding what is and is not valuable.
The show Caprica would seem to back this up, as it indicates that the cylons were created due to the hubris of one man and the fears his daughter had of dying, combined with his grief over her death and his unwillingness to face up to that or deal with it effectively. The fact that these events occur in the wake of terrorist acts responding to the onset of technology and the way in which that tech is replacing morality and theology is also relevant.
Battlestar Galactica at its end indicated that the value of a life lies in what choices the person makes with it, not in whether that person is human or cylon--not in how they were made or with what intention, but in whether they learn from their mistakes and try to be better than those who came before. That's a profound message, and making the choice to grow and change surely represents a revolutionary stance within a society so afraid of death and loss and change that it relies increasingly on technology to combat death.
So I think that most of our main characters are the joker and the thief, though some of them--notably Kara Thrace and Boomer--also serve as the princely court at various times out of their own fear.
I think the show indicated ultimately that the cylon rebellion was inevitable and that the destruction of the human civilization was ultimately necessary to create a more ordered, kinder and more moral society, one where Adama and Roslin could at last rise to roles in which they excelled and where cylons who opted to claim their humanity could do so.
I think that the use of this song represented Moore's last attempt to get this message through to us--his suggestion that we, like the humans of Caprica, would destroy our civilization if we kept going as we are, and that this destruction would be necessary to make way for rebirth.