yes - you can. this works "out of the box" for safari (ie - if you add facebook, you'll have to go through friction to reach facebook.com on safari without doing anything else.)

we just added support for chrome and other browsers by allowing you to associate domains with apps you've added. so associating facebok.com with your facebook app applies that same friction regardless of browser now.

When I had it block the Twitter mobile app, it also blocked twitter.com - I assume the same thing will happen if you block Facebook. The founders have mentioned they're adding support for blocking specific websites soon.