In general, scientific progress calls for no more than the absorption and elaboration of new ideas- and this is a call most scientists are happy to heed.
The basic idea is to shove all fundamental difficulties onto the neutron and to do quantum mechanics in the nucleus.
I think that modern physics has definitely decided in favor of Plato. In fact the smallest units of matter are not physical objects in the ordinary sense; they are forms, ideas which can be expressed unambiguously only in mathematical language.
The structure underlying the phenomena is not given by material objects like the atoms of Democritus but by the form that determines the material objects. The Ideas are more fundamental than the objects.
After the conversations about Indian philosophy, some of the ideas of Quantum Physics that had seemed so crazy suddenly made much more sense.