Al vs. Whole Milk

So I was waiting anxiously all last week until Al turned one so I could switch him to whole milk and stop buying that expensive and very unappealing (to me) formula. Al was not quite as ready as I was. The first time I gave him milk it was in a bottle (his preferred method of delivery) and he totally rejected it. SO I reluctantly went to half milk/half formula which he didnt mind at all. By wednesday I had him on 2 oz formula and 6 oz milk mixed together and he would take it just fine and even took plain ol milk from a sippy cup during the day. Then came Friday. He woke up (now stop reading if you dont like gross descriptions) covered in diarrhea. He then proceeded to do it twice more in a one hour period that morning at the daycare, soaking his play pin. Poor baby.
I have NO idea what to do now. The doctor says to lay off milk for a while ( um, ok, what the hell does that mean) and what am I supposed to do in the mean time? I give him yogurt and cheese, so I am not worried about his calcium and Vit D intake, but I am worried that he is not getting enough calories. He woke up last night at 12 starving and downed an 8oz bottle of formula. I hate milk.
One postitive is Al loves water (especially with ice) so fluids have not been a problem.
The battle goes on...