The problem got even more complicated. Now i'm trying to just delete any file, and i can't do that whether i have trashing enabled or not:

~/.emacs.d $ (require 'em-tramp)

em-tramp

~/.emacs.d [1] $ eshell/sudo touch /usr/local/bin/test-file

~/.emacs.d $ eshell/sudo rm /usr/local/bin/test-file

Removing old name: Permission denied, /usr/local/bin/test-file