Dear Benjamin, If I understand well, it is the same issue than the one reported here: https://github.com/alezost/guix.el/issues/28
Recently, Alex explained why in the second part of this message: https://lists.gnu.org/archive/html/help-guix/2019-01/msg00020.html One (not-yet satisfactory) fix seems to install guix itself in the profile: guix package -i guix then to correctly add ~/.config/guix/current/. It works for me. Hope that help. All the best, simon