The "Enable jQuery/Bootstrap" setting should remove that file from being included. I'm not sure why it would still be there if you disabled that.
JFBConnect does require that both jQuery and Bootstrap are loaded into your site. However, if you already have that taken care of on all pages, you can disable our inclusion.
Just for reference, yes, Joomla 3.0 does include the jQuery/Bootstrap libraries. However, not all extensions use that copy, which makes things very difficult for us. Additionally, if the bootstrap.js file is loaded twice on a page (once by Joomla and another by a 3rd party extension), *neither* will work. Bootstrap absolutely can't be loaded twice. Because of those oddities, JFBConnect has it's own specialized version of jQuery/Bootstrap which only works with JFBConnect. Yes, it means more page size, but it also means that it just works and other extensions can't conflict with it.
We're working to improve our Javascript and CSS loading over the next few releases to optimize things and decrease page load speed.
I hope that helps explain, but should you have any other questions, just let me know.
Thanks,
Alex