An article by The Green Lantern at Slate points out that while the carbon footprint left by producing milk is greater than the one produced in making soy milk, it's not by that much. Though soy milk isn't produced by cows, the genetic engineering that goes into making soybeans isn't anything to brag about.

Clearly the only solution to this problem is to stop drinking milk, thereby reducing many kinds of pollution. By eliminating milk altogether, we don't need to waste so much energy on cows, soybeans, cars for transporting milk, and making people taller. Height pollution is just as much of a problem as the others.