Sure, mathematical thinking can be useful, but it's only one type of logical thinking among many types which can be applied to programming.
I've been programming so much for so long now that before I even start writing code my mind launches into an esoteric process of reasoning that I'm not confident would be considered "thinking in math" since I'm not formally skilled in mathematics. It's all just flashes of algorithms, data structures, potential modifications, moving pieces, how they all affect each other and what happens to the entire entangled web when you alter something. Fortunately, my colleagues are often pleased and sometimes even impressed with my code, and yet I'm not so sure I would consider my process "thinking in math."
So, this isn't necessarily a direct refutation to the article. In fact, maybe what I'm talking about is the same thing as what this article is talking about. But, anyway, my point is that I feel that there's more ways to think about problems and solutions than pushing the agenda of applying formal mathematics.
As an aside, I noticed this part of the article:
"Notice that steps 1 and 2 are the ones that take most of our time, ability, and effort. At the same time, these steps don’t lend themselves to programming languages. That doesn’t stop programmers from attempting to solve them in their editor"
Is this really a common thing? How can you try to implement something without first having had thought of the solution?