I don't believe that Emacs is dead at all. Actually, most of the problems (multithreading, libraries, file I/O) raised by this article can be solved by replacing Emacs Lisp backend with Guile, which is an active and promising project [1,2]. As for Emacs philosophy, it might even survive Emacs (in the hypothetical situation where Emacs dies) if a project such as Emacsy (the second one presented in [1]) takes off. [1]…
Why guile, which has exactly zero usage outside a few GNUtoys. Why not, e.g. Racket? If you're going to go the trouble, _get it right_.
Back in 2002, the better choice was Common Lisp. One of CLISP's authors even made it work with Emacs over the course of a week-end [1].
There's never going to be the perfect fit for an embedded extension language. Hey, wasn't that what Lua wanted to be, and Tcl before it? Guile certainly isn't the easiest fit, but it's the only one that will get accepted.
At least, if they slowly change the actual extension language away from ELisp, all extensions that rely on external programs will survive better.
[1]: http://lists.gnu.org/archive/html/emacs-devel/2002-08/msg000...