I've had good experience with Apple support and warranties. I am told that the way they define 'accidental damage' for portables is by case damage. If the case is broke, then you dropped it and its your fault, if not, then it'll be on warranty.

And anyway, you might have slept through the storm (I slept through the '87 London hurricane!) and it would just seem to be a flawed part. How are you or they to know that it was in fact the lightening?