JFBConnect includes the Facebook Javascript API on pages to allow for adding the Like buttons and for authentication that uses the Facebook popup window. The iFrame you're talking about is what allows your users to interact with features from Facebook, like the Like button or authentication process.
If you aren't using any of the Facebook social widgets and you use the server-side login process, where the user is redirected to Facebook to login instead of in an authentication popup, then the Facebook Javascript API isn't required. We have it on our to-do list to strip out Javascript when it's not being used on the page. It's harder than it sounds though due to the numerous ways we allow users to add the social buttons, but it is something we plan to have in a release later this year.
I hope that helps explain, but if you need anything else, please let us know.
Thanks,
Alex