To clear some confusion : the French state owns the building and the Church is given use of it for cultural, historical and patrimonial considerations (it's just better for a building to keep its original use on-going if you want it to survive as best as possible). In that framework, it's normal for the religious authorities to decide of the interior decoration to the extent it's impermanent.

The article makes it sound much worse than it is. The truth is the Church makes stylistic choices that some people (including myself) don't like and they end up making a fuss about it.