I'm not endorsing what they do, but Cloudflare isn't the only option for DDOS protection. If you take them out now, you'll probably just send them deeper into the decentralized web, which is probably not a mutually amicable solution.
They well might be, realistically. Other similarly-atrocious sites that were eventually shut down by Cloudflare had a lot of trouble finding new hosts.
In addition, the dark web would result in them losing a large portion of their user base, both at the initial switch over, but also over time as existing members leave.
Decentralized =/= dark web. Who's going to stop them from setting up a Mastodon instance, or making an invite-only Matrix server?