I understand that you have to comply with law enforcement, but actively attacking the users of one of your customer's websites is super rude.
The more of the Internet you've got running through your service, the more appealing a target you are for not only domestic government pressure, but attempts from foreign state actors to compromise the service (through not only hacking, but espionage and blackmail as well).
It's not great.
It seems therefore entirely plausable that the admin handed they keys to the castle to the FBI anyway, or at least gave Cloudflare the okay to go ahead.
I can't find a shred of evidence that Cloudflare were involved directly in making the phishing page or even complying with the FBI.
Also I feel like Raid Forums is a bit mis-characterized in the article. It was largely a forum for people who collect OSINT about breached websites, not really a market place, and in the years that I spent there, I never saw people selling actually carding details, like they claim in the article. I used it regularly for my day job.