Unfortunately, you can't. Most of the cost for issuing a certificate is incurred by Let's Encrypt whether or not it's being used anymore, so a feature like that is hard to justify for technical reasons.
The good news is, many of the domain's certificates were issued December 1. Since that rate limit is per week, you can start creating more tomorrow.
One certificate can contain up to 100 names, but the domain's certificates are all for 1 name each. There are also a number of duplicate certificates. Would it be possible to modify your workflow to use a small number of certificates for many names, and replace them less frequently?
You can also apply for a rate limit exemption on the page I linked to first, but you probably have other options.