To get an idea of what happens to old physics when new physics is discovered, realize that Newton's laws are still correct, and can be derived from QM. That's what you get when you do a good job of actually checking the truth with experiments. All theories have implicit tolerances embedded within the known precision of the experiments used to confirm them, and with these tolerances you can say "Newton's laws are right" without denying other, finer details. Similarly, scientists 1000 years from now will agree with everything we presently know about the Standard Model, because all of our beliefs are tempered by how closely we know our experiments are looking.
>Quantum entanglement
I should add that entanglement isn't "shaky" at all, it was predicted from the start and has been observed in countless experiments to date.