Pragmatically, you could run a cut down version of jQuery BS along side YUI. But if you are going to go to the effort of implementing jQuery, then what's the point? It's relatively easy to add the jQuery version:
1. So, get the JS from inside the 'js' folder of the archive from: http://getbootstrap.com/2.3.2/index.html.
2. Rename the '.min' version to use a middle underscore, i.e. 'bootstrap.min.js' -> 'bootstrap_min.js' as Moodle does not like periods in the middle of filenames.
3. In 'config.php' of the theme add:
'bootstrapbase' => array(
); // Exclude YUI Boostrap code.
I know it's a YUI module, but it's actually loaded another way - long story.
4. Create a 'jquery' folder in your theme's folder and place in there the 'bootstrap.js' file.
5. Still in the 'jquery' folder, create a file called 'plugins.php' with:
$plugins = array(
'bootstrap' => array('files' => array('bootstrap_min.js'))
6. At the top of your layout files add:
Changing 'YOURTHEMENAME' as appropriate.