But the wave DOES interact with individual atoms. And yes, it causes scattering.
Look at gases. The molecules in atmospheric or lower pressure gases are too far from another to allow light to interact with more than one molecule at a time, except on the rare occasions when molecules are undergoing collision.
The phases of light scattered from different air molecules are indeed out of phase.
Now, a wave of light encounters many air molecules over one wave. With the result that while the retarding/refracting effects of air molecules add up over many molecules, the scattered waves being out of phase undergo destructive interference. This is not complete because the positions of air molecules are random. There is Rayleigh scattering in air. But it is still relatively weak - much of the light can pass through long column of air and is left over from scattering, yet appreciably retarded.
I was actually thinking of solids and liquids (which have high refractive indices but isn't Rayleigh scattering due to polarisation of the molecules in a gas and not the atoms? It's an elastic scattering phenomenon and I don't know how atomic energy levels would work apart from at frequencies corresponding to line spectra.