How a classical electromagnetic wave emerges from innumerable photons can be seen in this blog entry. It is not simple, one needs quantum field theory to start with. One should get the interaction of a single photon with a crystal lattice , and one can get a quantum mechanical solution, which will give the probability of the photon to scatter or go through the crystal. Then one has to use the logic/math, outlined in the blog link above, to see how the classical beam with its diffraction would emerge
EDIT: what I am looking for is really an explanation about what interactions are the photons going through(like absorption and emission by molecules for example) that when we take all the photon's interactions into account give us the macroscopic picture of how light reflects and refracts.
Photons can interact with matter by
a) elastic scattering : only the angle changes and not the energy
b)inelastic scattering with the field of the matter they hit: in this case the frequency changes and thus the color.
c)absorption by atomic and molecular layers: in this case the photon disappears and no longer contributes to the light beam. The atom may de-excite and an equal frequency photon come out, but it will not longer be coherent with the light beam because the direction of emission will be different than the direction of the macroscopic beam.
So in reflection one can handwave of the individual photons scattering elastically and keeping the phases between them, and thus the images can be reflected.
In refraction though the quantum mechanical solutions have to come in so as to show that the scattered photons keep a coherence, and I cannot see how without solving for a specific lattice and summing up the individual photons one can handwave an index of refraction. See also the answer by Marek here. and this link here.