What is the cost of a refinery processing 1 million tons per year of crude?

You need to be a little more specific. Refine the crude into what? Gas, diesel, another oil based product? Also crude oil is typically measure in barrels not weight that being said your figure of 1 million tons is about 6.2 million barrels. To give you a comparative figure 8.9 million barrels are refined on a daily bases.