There's no one "right" way to do this; there are several options, and
you can pick the one you like best.

First of all, the solution you came up with, renaming dired to
something else, might well be the best thing to do, and it is what
I've done the few times I've tried something like this.  Its advantage
is that it is very easy to back out of.  The way I'd recommend doing
it is loading dired, then evaluating

(fset 'my-dired (symbol-function 'dired)) ;you might not need the
quote on my-dired, I don't remember offhand.  Then rebind dired as you
see fit.  You might even want to write a dired function that chooses
the appropriate function depending on a variable you set.  This might
be best in light of the fact that you want to be able to type M-x
dired; then you can check using (interactive-p) whether or not it was
called from top level or from some other function such as find-file.

Another thing you can do is find where find-file-run-dired is called;
it should be inside find-file or some other function, which is
probably in files.el.  You can use tags to find it; simply type M-.
(meta-point) and when it asks you for a tags filename, give it
/usr/athena/lib/gnuemacs/lisp/TAGS (there ought to be a tags file
there -- if not, I trust that the next release will have one).  Look
around for find-file-run-dired; it shouldn't be too hard to tell where
dired is called.  Then rewrite the function and put it in your .emacs
file.

Which option should you choose?  I'd recommend the first (the one you
call "kludgy") since it's easier to undo -- just pop the function
definition back and forth between the two functions.

BTW, just for my curiosity, are you using monkey or direx?  I've
played with monkey a bit but have never gotten around to installing it
in my .emacs file (it seems to be rather heavy-weight when you just
want to edit a file, and it seems to completely take over my emacs),
but I haven't seen direx and I don't know anything about it.

I really wouldn't worry about cleanliness or portability here.  The
top level interface to dired isn't about to change in an incompatible
way, and you aren't going to support anyone else.  Your concern is to
configure your own emacs as you see fit.  I get the idea that you want
to keep both direds around and be able to pop between them.

Hope this helps...

Robert Krawitz / SIPB / OLC Volunteer