Detonating a few megatons right outside the earths atmosphere is unlikely to do anything at all to the people on the surface*, given that we spend every day with something just as hot and radioactive shining down at us. (Though perhaps looking up at the explosion would be a bad idea.)
And this plan calls for the nukes to be detonated when the asteroid is still a year, or years, away, read, out by mars.** (The Martians may take exception to this of course, their atmosphere is a lot thinner than ours.)
It's a comforting thought that had Apophis been a real threat***, we would have been prepared.
*Except disrupt the communication satellites.
**Not really mars, but you get the idea.
***I have a sneaking suspicion that Apophis is a very very real threat, and that everybody is lying to us to avoid panic while NASA quietly goes about handling it. Mostly because I wouldn't tell people in that situation either. We are of course, all going to die as a result of this plan, because NASA is going to get its funding cut off at a critical moment by some idiot group of senators that don't know what's going on.