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Unfortunately, there is no chemical control/fungicide available to combat this disease. Cultural controls include pruning of infected branches to prevent the spread of the disease to the main trunk. Once it gets to the trunk, it will eventually encircle the whole trunk and the tree will die. It sounds like it is too late to save this tree since you say that the rust has already reached the trunk.
It might be worth it to call Bartlett Tree Experts (http://www.bartlett.com/) and have them come out to look at your tree just to confirm the diagnosis of white pine blister rust and make sure there is nothing that can be done to save your tree.