I've heard the timing is because if you have a stomach full of food, the Carafate coats the food, rather than your stomach. I suggest you call the pharmacist. They're even more knowledgeable than the docs about these things.
My guess is that it doesn't take long for the protein drink to make it through the stomach, so you could take the Carafate sooner.
I do remember speaking to the pharmacist and she said that after taking meds, they should clear your stomach by the one hour mark, so you can safely take it sooner than the two hours, but if you take the Carafate, you need to wait the 2 hours afterward for the meds. You only need to wait one hour after Carafate before you eat, though.
2oz of protein drink shouldn't really interfere with the Carafate, but to be safe, the pharmacist should be consulted. Let me know what he/she says!