There's also the issue of using a weapon over heavily populated areas and at low altitude. Shooting down a missile will probably take place at high altitude. It's also possible, or even likely, that it will take place over a sparsely populated area or war zone. It could even be over an ocean. The laser might even be fired upwards. If you're shooting down birds from a plane there's a good chance you're going to be firing a laser outward or downward. What if you miss and start blasting holes through nearby buildings?
Bird strikes tend to be a problem most often during takeoff and landing-- usually at either end of the runway. Planes gain altitude so quickly that it's rarely a problem outside of a couple short windows as the plane is approaching or leaving the runway area. I remember reading about an airport with an especially bad bird problem that had success using dogs to keep birds away from the runways.
I think there is a simple solution to this. It might even be possible to put plants or grass around the runway that birds don't like. What about something with thorns that will be difficult for a bird to perch on? Or maybe something with a particular scent that birds will stay away from?