MooTools is being loaded as a dependency only when it's required (form
validation for example).
So if you manage to disable (to not load) it, requiring script will
break.
There's GSOC 2013 project to refactor scripts using MooTools to jQuery
(
http://docs.joomla.org/
GSOC_2013_Project_Ideas#Project:_Convert_JavaScript_from_MooTools_to_jQuery)
but as it says, it will be done after the summer.
At the moment Joomla is checking on scripts in /templates/[template]/
js/ folder before loading from media/system/js/ so you could put
jQuery alternatives of MooTools scripts in there but these should have
similar API and behavior.
For example: rewrite validate.js script to jQuery and save it in /
temnplates/[template]/js/validate.js
I'm actually doing the opposite for Bootstrap plugins :)