I was kind of surprised to see the Gov just disappear. I'm sure he'll be back but was definitely expecting him to head straight back to the prison with whoever he had left. Although he couldn't have known at the time it could have been devastating for Rick' s group since their best fighters went off to Woodbury to chase him down.
As for Carl, I think he did the right thing, given the circumstance... The kid didn't drop the gun and was slowly approaching. With a shotgun that could have been very bad juju..