First of all, the paper that this article is reporting on doesn't actually prove a separation between quantum and classical algorithms at all. It's an oracle separation result, which makes it an important result in complexity theory, but not a statement about actual classical or quantum algorithms.
Second, the result is unrelated to the Church-Turing thesis in the first place, since it's only about relative efficiency, whereas the Church-Turing thesis is about computability.
Every quantum algorithm can be simulated by a classical computer, so quantum computing cannot possibly disprove the Church-Turing thesis. However, there's a stronger variant of the Church-Turing thesis which also takes performance into account, and it's plausible that quantum computers can contradict this stronger version (although we're very far away from actually proving that).
Second, the result is unrelated to the Church-Turing thesis in the first place, since it's only about relative efficiency, whereas the Church-Turing thesis is about computability.
Every quantum algorithm can be simulated by a classical computer, so quantum computing cannot possibly disprove the Church-Turing thesis. However, there's a stronger variant of the Church-Turing thesis which also takes performance into account, and it's plausible that quantum computers can contradict this stronger version (although we're very far away from actually proving that).