You break it up into small enough fragments and most of that kinetic energy will be absorbed by the outer atmosphere which has precious little direct interaction with the lower atmosphere and surface anyway. However, I suspect it is largely a moot point. How exactly is one supposed to insure uniform breakup of what is essentially a flying mountain? Whatever your breakup mechanism, it will almost certainly create a distribution of new particle sizes. Some will be small enough for the atmosphere to handle, but you'll still end up with quite a few monsters. And I still don't see how exactly is one going to achieve any significant breakup in the first place? Deflection is almost certainly a better bet.
... I wonder what could be accomplished with a very large (several kilometers wide) diffraction lens used to focus some serious sunlight on the subject? In Earth orbit, sunlight has about 1366 W/m2. Take one square kilometer of that and focus it on an area 1 meter wide... 1.366 gigawatts over a square meter. yEAH! I had been thinking of using sharp thermal gradients to cause fracture, but with that much heat the resultant outgasing might have a significant effect on its trajectory.
Now that is starting to sound like fun. What would it take to build something like that?
