Oo, tough one.
I guess you can argue that his punishment is undeserved in the way he has been manipulated by Meph. Faustus starts out with impressive aims, for example, wanting to make Germany secure: "wall all Germany with brass". He is unable to achieve such aims through Meph's continual advice to pursue less meaningful acts. In this way, he has been 'tricked' out of the power he had been promised. How can he repent if he has not truly sinned? Granted, Meph does warn him of the "hell" he faces.
It is an interesting point you raise: "They punish him for what - attempting to quench his Renaissance desires?"
I had not thought of it in that way. Perhaps he can be seen as a brave and enviable man, who simply has an insatiable desire for knowledge. How can you punish a man for simply trying to expand his grasps on the human limits? A brilliant point for any transgression essays, with plenty of counter-arguments too.