Erm, yes you can. Free movement in normal situation and close-down during times of severe disease are two entirely different scenarios.
Either way, screening is already happening as people board in affected countries, but by the time they land at their destination their condition could have changed dramatically.
So what, you're going to pay to have border staff sit around twiddling their thumbs for years during a "normal situation"? Or you're plan is to recruit and train however many you need when something like Ebola kicks off?