This is the real issue with not allowing wildcard certs. If the rate limits were something that just cut in at abuse-levels, there'd be no need for them. Sites with per-user subdomains (to get security features like cookie isolation, break same-origin effects, etc) run into the limits really quickly, and must currently rely on a wildcard.

I've been calling this "the tumblr scenario", but people seem to think there's a way around it without just using another CA.

I deploy all the different little code projects I make to different domains and I've hit the Let's Encrypt rate limit. If (like me) you waited a couple months to secure these little side projects, you'll hit the rate limit too. That being said, I just waited a week -- now everything is secure.

I'd imagine you might be able to reach out to them in that case.