what if their email address is @ the domain

Even if cloudflare stopped publishing the correct MX records for a domain, wouldn't Cloudflare still be able to send email to the MX server that had been specified? Seems like email should at worst be down for everyone but Cloudflare.

Well, that's poor planning on the user's part. In this case the OP stated he registered using a gmail address.

If the only contact information the registrar has is the @ of the domain then that likely mean that the registrar is failing the contractual obligations that exist between the registry and registrar. While I have not read the exact contract that exist for .com registrars, I am confident enough to say that you can not do that.

The OP made it clear that he used a gmail account for contact so there was no excuse for him to have not received a message regarding the deletion of his domain records.

I think it's pretty common advice that anything domain-related needs to be a different email. I've heard that, and I've only ever admin'd my personal domain. For exactly that reason I registered for Cloudflare with a gmail account.

Also display a prominent notification in the web interface then.