Does anyone know the consequences of killing the harpers. I get attacked by more harpers as soon as I leave the city after wiping out the harpers guild. Is this going to keep happening through out the game ?

I'm guessing this is part of Jaheira's quest. If you're fighting Harpers that Jaheira keeps talking to, then there's nothing wrong. If you wiped out the Harpers guild because you just don't like Harpers, I'd say there's a good chance you're going to be hunted by them forever more.