For what it is worth, I dug around on this subject quite a bit many months ago (I think I even have a thread on this board somewhere about it) while planning what is now a shortly-upcoming trip (September 2015). Basically I arrived at the same conclusion. Our trip begins in Budapest and after the conclusion of our stay there we are picking up a car to enable us to explore Slovakia and make our way through the Tatras and over to Krakow. Yes, the one-way cross-border fees are very high, but they are a cost of doing business, and they seemed to pale in comparison to the cost in time and freedom to explore that would be incurred trying to use transit in that region. Once you arrive in Krakow you can, as others have said, be rid of the car immediately at that point. I think you have made the right choice.