As I understood it, the goal is not to simply allow Guile alongside Elisp, with the intent to confuse users, but to eventually replace Elisp completely. Guile devs are claiming that their Elisp implementation running on top of guile provides several substantial benefits over Emacs own C-implementation of elisp:
* higher speed
* native threads
* lexical scope
* ffi
* module system
* goops, guiles object system
Emacs is a key GNU project, but to the detriment of the overall project philosophy, it uses an extension language no other GNU project uses and never will use. Elisp may be working for emacs, but it is isolating it from all other apps, since nobody else uses Elisp. The long term goal of GNU is to "emacsify" the whole system, i.e. to enable emacs and other apps to talk to each other over guile es their universal scripting interface.