Incidentally, moving out of reach of NSLs just means you're now in the reach of the CIA/NSA with no need for a warrant.
And within the reach of other governments likely to be equally (if not more) meddlesome.
How would one move beyond the reach of NSLs?
I presume the OP meant moving LetsEncrypt to an organization that's in a more privacy-friendly jurisdiction.
Which isn't what's happening here. What's being transferred to the EFF is not the whole service, but one specific piece of client software which interacts with the service.
Indeed, and feel free to use or develop a different one if you prefer. We'll help you publicize it!