Lazs, the question is, how much of the central authority is inherent in their government, and how much is a secondary result of the Cylon attack? Characters like Tom Zarek (Richard Hatch) seem to suggest that there's a lot of resistance to the heavy handed, authoritarian government that Roslyn set up.
The real problem, it seems, is that they need the centralized control of a fleet captain because of the immediate threat of the Cylons, and at the same time they need civilian control to set long term objectives as to the direction the survivors will go. That's why the conflict between Roslyn and Adama was so great.
I bet Zarek will be the new leader, and he'll butt heads spectacularly with Adama.