With that kind of number, you're pretty much guaranteed some elisp is going to stick around forever (especially considering Emacs' glacial [but improving!] rate of change).
So yeah, it's not so much the Elisp in the Emacs source that's the problem, it's how do the maintainers switch to maintaining Elisp inside of the Guile project (up until now, Elisp was maintained as a language alongside Emacs). At the very least, this is how I understand it.
Yes, there is no way Emacs will get rid of elisp. That's why Guile Emacs includes writing an elisp frontend for Guile. (There is also a Frontend for ECMAScript and an experimental one for Lua)