Einstein did not say that Newtonian mechanics was wrong, special and general relativity reaffirm it within its domain of application, he showed that this domain is restricted, namely Newtonian mechanics does not apply to objects moving at speeds close to the speed of light, or in strong gravitational fields. Absolute space and time were part of Newton's philosophical interpretation of his theory rather than part of the theory itself. As for anti-semitism it was common in Europe for centuries, and especially prominent at the time due to the rise of Nazism, so Einstein's science was less important than his race.
Can some elements of modern scientific theories be eventually abandoned? Certainly, especially interpretational parts, even big ones. For example, consider a common belief of late 19th century as expressed by Michelson in 1902:"The day seems not far distant when the converging lines from many apparently remote regions of thought will meet... Then the nature of the atoms, and the forces called into play in their chemical union... the explanation of cohesion, elasticity, and gravitation — all these will be marshaled into a single compact and consistent body of scientific knowledge... one of the grandest generalizations of modern science ... that all the phenomena of the physical universe are only different manifestations of the various modes of motion of one all-pervading substance — the ether." Ironically, it was Michelson's own experiment that eventually led Einstein to reject ether, and the absolute space it embodied.
But Maxwell's electrodynamics, which was originally phrased in terms of ether, was not only retained but became a foundation for special relativity. Because empirical evidence which it proved to describe and organize did not change, only its interpretation did. The same goes for proven modern theories. We may discover that they do not apply universally (in fact, we already know that general relativity and quantum mechanics do not), or choose to revise some of their concepts, but they will still describe the phenomena that they proved to describe. This goes for E=mc² just as for Newtonian mechanics and Maxwell's electrodynamics. How it manifests itself in gravitational bending of light or splitting of the atom will remain true in whatever theory that replaces Einstein's, see What were the early empirical tests of Einstein's mass-energy equivalence $E=mc^2$?