How would Netlify feel about not being able to issue or renew any certs for any sites for a month? Plenty of platforms rely on LE exclusively for one-click/automatic HTTPS for their customers sites.
The thing is that we're not talking downtime here, but rather something in the CA compromised, which would mean that pretty much ANY website could be impersonated, as the attacker could issue a Let's Encrypt CA valid certificate for it. That is mitigated by invalidating this CA, but that also invalidates all legit certificates previously issued by them. So they need to reissue them all
You can both block certs that do not appear in the logs, and decide which certs not to trust ("everything after Friday the 13th at midnight is not trusted"), once you know the date/time of the intrusion.
What exactly is the issue with centralization here?