A centrifuge essentially creates pressure, according to the relation a*x, where a is the acceleration of the centrifuge, and x is the position. This is equivalent to the formula P = g*d for hydrodynamics, where d is the depth.
[clarification]This is imagining a liquid or gasseous sample, in a test-tube in a centrifuge, being spun around. The liquid will be under pressure - the greater the depth, the higher the pressure. The rotor of the centrifuge on the other hand, will be in tension.
You can replace a*x by \int a(x) dx in the case where the acceleration variews with position.
There will probably be some very small effects on the orbits of the electrons as the pressure increases. I haven't worked out the equations, but intuition suggests that they will become oval rather than circular.
As a practical matter, you can't rip atoms apart in a centrifuge because the rotor is built of atoms. The bonds between atoms will fail before the atoms themselves do, causing the rotor of the centrifuge to fail. But you can look at what happens to matter under high pressure by looking at high gravity situations, like the interior of Jupiter and the surface and interior of stars.
Atoms do not exactly "rip apart" in these circumstances, but given enough pressure, normal matter will turn into electron degnerate matter, white dwarf star material.
What basically happens in this case is that rather than have electrons orbiting individual nucleii, you have a "sea" of electrons, not associated with any particular nucleus, with the nucleii scattered throughout the "sea" of electrons.
To create this state of affairs requires enormous pressures, but it will happen under extreme conditions such as the interior of a white dwarf. (Further reading suggests that metallic hydrogen, thought to be found at the core of Jupiter, may also be a form of electron degenerate matter, though I'm not terribly familiar with it or its properties. Corrections on this point are welcome.)
For more info, see for instance the wikipedia article
http://en.wikipedia.org/wiki/Degenerate_matter
As Wiki mentions, it is the Pauli exclusion principle that keeps electrons normally form intermingling with the nucleii of any atom other than "their own". When the pressure becomes high enough the Pauli force is not large enough to exclude electrons from inter-penetrating, and we get degenerate matter.