Many words have lost their original meaning over the centuries. The Romans in England referred to the "farming" community as Pagan. "Country people",bumpkins,uneducated,peasants.
Heathen merely meant a person who lives on the Heath (Moorland). They usually kept pigs, and did not "till" the land. These were also looked upon by the Romans as "Un-sophisticated",dim-witted.
With the rise of Christianity both words were corrupted to mean "non believers, idolaters, Godless".
Those meanings still exist today. Such is the power of the Catholic Church. It was they who started to use those words to condemn.