In addition to the HTTP-01 challenge type (requiring adding a file to the
/.well-known/acme-challenge directory) there is also the TLS-SNI-01 and DNS-01 challenge types. Neither of these require changing content in the webroot and would likely be viable options for your situation.
Let’s Encrypt implements the ACME protocol, an IETF draft. The challenge types are defined by this protocol and so this is really first and foremost an ACME feature request not a Let’s Encrypt feature request
That said, I believe email validation was discussed in the early days of the protocol and purposefully not included. It seems unlikely that it will be added now (or that Let’s Encrypt would adopt that challenge type if it were specified). Email validation is typically considered to be one of the weaker forms of domain validation. I would definitely encourage you to evaluate TLS-SNI-01 and DNS-01 challenges for your environment.
If you specify more information about the server OS, webserver software, and ACME client you’re using folks will likely have more concrete advice on how to proceed.