I can imagine a situation where a proto-cat was omniverous but would be better off being a pure carnivore, and this was the adaptation that pushed it to be a pure carnivore.

Why might that happen? Inventing something off of the top of my head, what if the proto-cat lived in an environment with a sweet fruit around that was bad for cats. An adaptation to make them not be tempted could then be adaptive, with the side effect that they became purely carnivorous.

The odds are against this particular theory. Atrophying is more likely. (The fact that many other species have specialized in being carnivores without such an adaptation is evidence that my "just so" story is unlikely in the real world.) But the scientist is correct to say that we don't know whether we're looking at a cause or an effect.

Cheers,
Ben