https://en.wikipedia.org/wiki/Ewald%E2%80%93Oseen_extinction...
In fact it appears that the isotopic dependence for silicon isotopes is known,
https://arxiv.org/abs/1105.0822
and the refractive index of Si 30 is lower than Si 28 in the IR, because of the different absorption lines.
https://en.wikipedia.org/wiki/Kramers%E2%80%93Kronig_relatio...
which have very far reaching effects in term of refraction (the real part of the permittivity decays as 1/w).
In term of resonances, it's important to note that the nuclei themselves are not neutral either. In the IR, the time dependence of the field is slow enough that the nuclei can follow it resonantly. Those fields are much below electronic resonances so the electrons aren't even contributing much beyond making the crystal stable!
Note you should clarify that by "slowing of light" you mean a lowering value of the absolute speed of light.
While Einstein assumed it was constant, yet said speed and time we're changing. It's actually simpler to say the opposite; speed and time change because speed of light (c) changes .