Atoms know very well that negative and positive charge are different
(it is always the positive charge that is in the nucleus, and the
negative charge outside). So do superconductors.
(normal metals don't, that's why they are not giant atoms).
The view that a superconductor is a giant atom is in fact not new; in many old papers one can find statements to that effect, for example:
London and London, Physica 2,341 (1935): "Wenn wir uns den Supraleiter als ein grosses diamagnetisches Atom vorstellen ..."
London , Phys.Rev. 51, 678 (1937): " ...the electromagnetic behavior of the superconductor as being the same as that of a single big diamagnetic atom"
Ginsburg, 'Fortschritte der Physik 1, 101 (1953): " Ein riesiges Atom von makroskopischen Abmessungen und mit einer entsprechend hohen Elektronenzahl wurde sich in einem Magnetfeld wie ein Supraleiter verhalten. "
Smith and Wilhelm, Rev.Mod.Phys. 4, 237 (1935): " equivalent to considering the body as a single large diamagnetic atom "
Slater, Phys.Rev. 52, 214 (1937): " being similar to large atoms, they have a large diamagnetism "
as well as in some of the older books:
Rickayzen, Theory of Superconductivity, (1965), p.217
"Thus an atom behaves as a superconductor in a small, uniform magnetic
field...a superconductor behaves like a large (macroscopic) atom".
However: we now have understood that the analogy is in fact much closer than originally thought: not only is the diamagnetic behavior of superconductors similar that of atoms, but also the charge distribution of superconductors is qualitatively similar to that of atoms: more positive charge near the center, more negative charge near the surface.
Indeed, superconductors expel negative charge (electrons) from their interior!
This is because holes are not like electrons , and ultimately because the proton is 2000 times heavier than the electron. Just like there are no electron-hole symmetric atoms, there are no electron-hole symmetric superconductors.
And the process by which the normal metal becomes a giant atom provides a dynamical explanation of the Meissner effect.
For more information see papers on
the theory of hole superconductivity.