Forgive me if this question has been asked before, but this is one of the only things about the show that I never understood. Watching the mini-series again made me think about it.
They knew there were Cylons in the fleet.
They knew the nebula or whatever it was surrounding Ragnar made Cylons sick.
They knew that the Cylons were not coming in after them. It seems that there was only one way into the nebula, so they could have shot anyone trying to fly in. Especially if they posted some Raptors to watch at each of the known turns.
They knew the war was over, and that they had lost.
They knew they were going to run and hide.
Why not wait for all Cylon infiltrators to get sick? It seems it would have only taken a day or two at most. Plus if you are going to hide, then having Cylons in your fleet is the very last thing you want, even for the short time while Baltar completes his Cylon detection test.
One other thing, why did they not cannibalize Ragnar station before they left? Future shortages could have easily been guessed, because there were always civilian ships asking for stuff. Plus it was a safe bet that they were the last humans alive.