In our case it would have been a total ballache to disable Cloudflare proxy. Just sorting out new SSL certs alone would have been a nightmare, not to mention all the page rules, security rules, etc that we use Cloudflare for. Plus changing firewall rules to allow our web servers to be exposed directly to the internet. Sucking it up for a few hours while the issue resolved itself was far more preferable.
Is it a recognised signed-off business continuity risk that you are dependent on a single company like that?
If CF decides they don't want your business, you are out of business? Are your page rules and security rules requirements?