I would use area rugs myself. I had the carpet removed from the family room and two of the three bedrooms. The formal living room is carpeted as is the masterbed room but I just love the hardwood floors.
My biggest recommendation for hardwood floors is the fact that it's so much cleaner. One doesn't realize how much "stuff" ends up in the carpet until it's gone and the "stuff" is seen resting on the hardwood floor. So much healthier in my mind.
But if you do put carpet down and get a new dog, just make sure to set up a routine in taking it out for it's walk, and stick to it. You might also designate a "potty area in a special area with newspapers on which to do the job" until fully housebroken.