Killing a brand name does nothing to influence the silicon itself. Others have said it, but it bears repeating.
The Atom processors suck for computing in a desktop environment. The tablets and ultra low end towers that used them were putting cost way before performance. On the other hand, the atom was an excellent file server. I could store all my iso images, my comics, videos, etc... and access them across the network without substantially bumping up the power bill. The atom made that possible.
As far as comparing the APU to an atom, there is no contest. An APU can hang with a moderate Intel CPU and low end dedicated graphics card, without losing in every category. That kind of performance is admirable, and something that the new atom (or whatever the rebrand is) is moving toward. It isn't there yet, but a little PR juju could allow the average consumer to be confused enough to think that it is. It isn't exactly Intel maintaining the high ground, but it will likely allow people to look at atom level performance as a good thing.