The following should unload the system installed auctex, it is mentioned in the manual here, try to have it early in your init file so that it is executed 'before any of its modes have been used'
(unload-feature 'tex-site)
This will actually work for any emacs package.
Also, will it be possible to set keys for default latex commands after that? For example, one user has following line in his .emacs file
You can wrap it in eval-after-load
so that the keybinding is set only on when the file is loaded. I do not use auctex, I am assuming that tex-site
is the name of the file that loads auctex
(eval-after-load 'tex-site
'(global-set-key "\M-]" 'tex-close-latex-block))