Let's Encrypt isn't interested in S/MIME. You are, of course, welcome to try to repurpose their software and/or the ACME protocol to provision S/MIME certificates.

Although S/MIME isn't a real Wild West like some types of X.509 certificates, it has seen much less oversight than SSL/TLS ("Web PKI") certificates. There's also not really a great appetite for cleaning it up. If you want to be the hero in this story there's definitely an opening for that.