I'm pretty sure I've seen laser protection glasses that work by blocking a very specific wavelength. Because they take such a small chunk out of the spectrum, they have little effect on other light sources. Something like that might work for windshields. (I guess you might need to block more than one frequency based on the types of laser that need countering, but probably not more than a few.)
Or maybe you could use the welding helmet technology with a trigger that responds only to very specific frequencies, so the windshield (hopefully) wouldn't go opaque with each lightning flash.