letsencrypt.org is not even working, and it seems to be Linux only, at least for now. What about other OSs?
Mozilla is one of the backers behind letsencrypt. I'm sure they won't be deprecating anything until well after it is up and running. This was an email to the Mozilla community asking for feedback, not an announcement of any major deprecations in the next version of Firefox.
Letsencrypt is based on an open protocol [1], I'm sure there will be implementations for all major platforms.