Today's update from Let's Encrypt did allude under "ACME Protocol Updates" that there might be further work done to the protocol to attempt to remediate the risks.
Probably they don't want to get specific because even if a concrete proposal were ready to begin coding today, it would take time to build the reference client, time to build server infrastructure, test, etc.
Then before that work would have any benefit to the various websites needing validation, it would require server software upgrades to facilitate those extensions or ALPN negotiations.
My utter speculation is that they're thinking it would likely take long enough that everyone will have to be off TLS-SNI-01 before its replacement becomes available.