In your template(s) just replace
<?php
// automatically include optional WB module files (frontend.css, frontend.js)
if (function_exists('register_frontend_modfiles')) {
register_frontend_modfiles('css');
register_frontend_modfiles('jquery');
register_frontend_modfiles('js');
}
?>
with
<?php
// automatically include optional WB module files (frontend.css, frontend.js)
if (function_exists('register_frontend_modfiles')) {
register_frontend_modfiles('css');
register_frontend_modfiles('js');
}
?>
Now WB doesn't load the internal jQuery stuff anymore, so you can add your own lines and preferred files.
As far as I know jQuery is not used in a the backend. If it's loaded anyway (I didn't check), just disable it and see what happens.