Same thing happened to my faction leader. He was a bearer for several years before it cleared up. Oddly enough he got it *again* later on. But that went away for good. He lead an amazing life really, lead numerous invasions, became a plague bearer twice, saw his empire double in size and become the richest and largest in europe.

Btw, the characters (generals/agents) seem to stay bearers long after people start dying. Don't worry... they'll lose plague bearer status eventually. Just don't move them into other settlements!