In your config in components array add
'clientScript' => array('scriptMap' => array('jquery.js' => false, ))
Then load what version you want in layout header:
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.9.0/jquery.min.js"></script>
For yii 1.1.13 and lower and for jquery 1.9+ you'll need to patch jquery.ba-bbq to resolve some conflicts.
What you did (manually remove jquery) is very bad. Revert this.
To exclude some scripts use scriptmap. It can be used in controller before actions render and in config file.
All global scripts (jquery,jquery-ui etc.) must be in header in main layout. Load only custom scripts or plugins in your views.