Well, a lot depends on what exactly that "Threat Prevention" setting is doing, and if there are any other settings for it that you can configure besides turning it on and off.
For instance, if all that's running on port 80 is a redirection to https and the challenge response for the Certificate Authority, generally one can just keep port 80 open to all. Or, you might be able to exclude the /.well-known/acme-challenge path from being blocked.
If your DNS server is configured to be more open than your web server, you might be able to switch to the DNS challenge.
Or, yes some people configure hooks in their ACME client to make their firewall less restrictive while renewing a certificate and set it back after the challenge is completed.
As the FAQ I linked says, the core of it is that Let's Encrypt needs to confirm that you control the domain name as seen by everywhere on the Internet, so you need to prove control over it as seen from everywhere on the Internet. Generally firewalls should be able to be configured to allow for you to prove control while blocking the things that you want to block.