Jason Bourne has "Lateral Thought," like most trained assassins. Though the professor lacks counter thoughts to Bourne's lateral thinking, the scene illustrates how to unconventionally solve and or create seemingly dire predicaments.
I say dire because it plays into the professor's blunder. In an intense situation like this, his flight or fight kicked in when it shouldn't have.
Bourne doesn't know how many assassins are in the field (as he asks the professor how many of them there are). Scattering the birds accomplishes several things. Bourne might be under the assumption that there is more than one killer, fires a shot to indicate that one of them was hit or spotted (if they're separated), to emotionally compromise their future decisions. Had the professor correctly decoded Bourne's move, I doubt that he would have left his position. That and, the gun that Bourne was using is distinguishable, and further feeds valuable information to the Professor.
Next, Bourne has a short range weapon. Scattering the birds may not only confuse the remaining assassins, but allow for him to get closer to them. If he had not scattered the birds first, then ran through the field, the birds would have given him his precise location.
My biggest problem with this is that the professor seems to lack lateral thinking. Of course it would be harder to showcase Bourne's character or hold on solving problems if their match was full of counter moves. Hard to see that he's good at solving problems if he keeps creating new ones. But it would have been interesting to see another versus with another assassin later on that could counter Bourne's moves.