Sorry for the delayed response. What you're asking for is actually becoming a bit more common of a question. We'll likely be making this response into a blog post or documentation article at some point.. so if you have any questions or suggestions, let me know.
Doing what you're looking for should be pretty easy with JFBConnect and our SCLogin module. Here's the basic steps you should need:
1) Go to the Joomla User Manager. Click the "Options" button. Under the "Component" tab, disable the "Allow User Registration" setting.
2) Go to the SCLogin module. Disable the "Show Login Form" setting. That should hide everything.
3) Go to the Plugin Manager. Find the "System - Remember Me" plugin. Disable it.
That should do what you're looking for. JFBConnect *should* still be able to create accounts, even though the Allow User Registration setting is disabled.. but please, please test to make sure I'm not mistaken. You can even continue using the Activation settings of the Joomla User manager, if you want users to verify their email or you want to approve them first. They just shouldn't be able to register through Joomla directly.
I hope that helps get you started, but if you need more information, just let me know!
Thanks,
Alex
Stripping Joomla Core Registration
