When you first get outside, do a Matrix jump and land on the first bar. Avoid moving or you will fall off. If you see the Agent, he will be punching nothing. This is a good time too refill health and Focus. Note: The Agent may fire at you.
While being chased by all the Agent Smith clones, get to the window which first leads you out to the scaffolding and climb out of it. Once on the scaffolding, grab a gun and hide around the corner. Once Agent Smith comes into firing range, fire through the window while hiding round the side so you can evade if he fires back. After emptying a round on him, he will stop, straighten his tie and jacket, and will not attack you, even if you hurt him.