Honestly the point of the article seems to be that changing canon is secondary to telling a really compelling sci-fi allegory story.
I think that's exactly the point, and it's one that is often disregarded.
And to be honest, the sudden retcon of the Cardassian wars is not very easy to square with the way the Federation was presented in early TNG, existing in an era of unprecedented peace. "Contradiction" might be a stretch, but it's inconsistent.
I've been sitting on an essay concept for a few years now, all about how TNG was secretly (and unintentionally) about the end of an era of peace, and the Federation being shocked out of complacency.
The retconned Cardassian war (and to a lesser extent, the Tzenkethi conflicts) is the biggest challenge to address, but their very existence kind of supports the underlying notion that things were never as good as is popularly believed.
All of which is neither here nor there, and I think your point is a good one.