When in the tower, and the Agent is shooting at you, quickly run down the left pillar and stand behind it. The helicopter should be at your back. Use your peek and shoot move to your left side. If you use a fast enough gun, you can kill the Agent in about three seconds. If you fail to kill him the first time, keep in mind he moves in this order: left, right, back. Stay behind the pillar and the your peek and shoot and you will not be hit.