You people don't seem to pay a lot of attention while watching the show, do you?. Maybe the whole thing is a bit unusual and some plots are a bit non-realistic but all in all everything looks good.
I guess you missed couple episodes where it was said how Joe was getting his followers. Prison inmates couldn't do it. Prison guards have done it once already. It would be stupid, as you wrote, to do it again in a short period of time. The whole penitentiary system would be on target by the police, FBI, SWAT, ATF and who knows what else.
Claire was saved by the FBI. She didn't run. It was Charlie who ran away but since FBI didn't know how many people were inside they said "they". Try not to fall asleep next time ;-)