Lee may well be in trouble for giving amnesty to the rebel cylons. It fits. Coupled with the foul mood everyone will be in for having their hopes crushed about Earth, it's plausible that there would be backlash. They irradiated our worlds, forced us into space to survive, there is no inhabitable Earth, and
you're giving them amnesty, Adama? Are you frakking kidding? I can imagine that factions amongst the colonials would resent Lee making that decision and, by extension, being angry at Bill for backing him up. If Earth had been lush and green and had people to welcome then, forgiveness (or at least tolerance) would have been easier to come by. Zarek exploiting such a situation is also extremely plausible.