My answer to your question is, "No," it should not hurt to play after as much time as you've put in. The first guitar I owned hurt my fingers and nothing changed that; it just wasn't a good enough guitar with respect to action. Good enough action does not need to mean expensive. Anyway, think about going down to the music store and playing a few guitars--see if it makes a difference. Another thing you could do is have the luthier at your favorite store take a look at it.