Punishing the DNS resolver is weird. Would you punish the phone book company for having the number of a criminal listed?

Same reason copyright abusers threaten people that help remove the DRM from their Amazon-bought e-book so it can be read on their non-Amazon bought e-reader with a $250,000 fine and five years in prison for circumventing a digital lock using DMCA, because it's what the legal API allows them to achieve their end goal.

It's not about if it makes sense from a moral point of view.

The most likely answer is that they didn't think about it or didn't understand or didn't care. But on the off chance they did, perhaps they thought the DNS provider would enforce the ruling worldwide.

It is actually worse than that. This amounts to punishing someone for looking up a phone number in a phone book that someone else published.

It shows maliciousness (we can bully this smaller player for a win) and/or total incompetence (we don't even understand how internet works, but we'll issue rulings anyway).

Because they can.

Attacking the people doing the actual bad things is hard, attacking a single unified organization is easy.

If phone book publishing were regulated in a way that paid content on the internet is regulated, then absolutely yes. Not only that, people who mention the existence of phone books as means to obtain phone numbers, and people developing software capable of storing phone numbers, would be threatened and harassed too, as enablers of criminal activity. Copyright leeches have enough money to buy laws favorable to them. Which, also, gives them more money to buy even more laws favorable to them. It doesn't have to make sense for you because it's not designed to serve your interests.

The same method is used to block sites that don't respect the decisions the French people have made regarding the limits of the freedom of speech (no hate speech, no terrorist proselytism, no pedo, etc.).

Granted, that's the theory.

When the demands come from a company on the basis of copyright/intellectual property (that is, exclusive broadcasting rights), one can feel less comfortable about this affair; even thought the judgement mentions that the case is backed by the ARCOM, the french authority for broadcasting, which should instead IMHO deal with a couple or two of private TV channels that are obvious vectors of fake news.

But, this is the same copyright that can protect you when you publish programs, source code, images, etc., even when you use a free and open license; the licence has meaning thanks to the copyright.

Sue the government for providing the road that criminals walk on!

You would if you could and it'd probably work.

I believe the position of the French government is that anyone in the path of a crime can be ordered to block the part of the crime that relates to them, without having any liability for the crime. So quad9 are not criminals for not blocking pirate sites, but still have to block specific sites when ordered.