Please upgrade to JFBConnect v6.2.1. It was just released on Monday, but should help you accomplish what you're looking to do. In that release, in the JFBConnect->Configuration area, are 2 settings:
* Load jQuery/Bootstrap
* Load Bootstrap CSS
Set both to "No" and those files shouldn't be loaded anymore. The Bootstrap CSS option was just added in 6.2.0, so you wouldn't have seen it before.
I hope that helps, but if you still have issues, just let me know.
Thanks,
Alex