The key claim in the article, that gradient descent could not discover physics from equations seems, like it is a statement about neural networks, not gradient descent. Given sufficient training data, a neural network can probably learn to model physics. I sympathize with the concern that it's very difficult to translate a neural network's knowledge into human concepts, but I see no reason to believe that optimizing the same system with an evolutionary algorithm would make this problem any easier. You could e.g. try to do program induction (which was supposed to be the future of AI many decades ago) instead of modeling the data directly, but choosing to perform program induction does not preclude the use of a neural network. Neural networks trained by gradient descent can generate ASTs (e.g. http://nlp.cs.berkeley.edu/pubs/Rabinovich-Stern-Klein_2017_...).
[Edited to remove reference to universal approximation; as comments point out, even if a neural network can approximate a function, it isn't guaranteed to be able to learn it. But I am reasonably confident that a neural network can learn Newton's second law.]