My mom and I stayed at the King Alfred Pub in 2011 and quite enjoyed it. It's a real locals' pub with very nice (not fancy), clean rooms overhead. The owner and staff were very accommodating and friendly, and a delicious breakfast was served in the dining room. We ate dinner in the pub a couple of evenings, which was very nice - both in terms of convenience and quality of the food.
A very good friend of mine teaches at the university, and it isn't actually that new - used to be King Alfred College! I love Winchester - lucky you to have a son in university there.