If you believe in the ideals of a Democratic Society, you have to side with Zarek, as he is the ONLY Democratically elected representative, being a VP on the Baltar ticket, whereas Roslin as president the second time was essentially a coup.
If you are a realist, you side with Adama, in that this hasn’t been a Democratic society for more than 5 years, and a small dictatorship probably is the best chance for survival.
Frankly, after this rebellion, I think the powers that be need to admit to themselves and the fleet that Human Civilization is no longer a Democracy, and deal with what it has become.