I'm with Jeff on this one. While I agree that Jetpack is indeed full of features that one might not need - some call it bloated - I don't see this as the way to go. Not unless the modules add some extra functionality, that is?

It is already possible with Jetpack to activate and deactivate modules, and if there are some modules that you just don't want to be activated on your site, ever, you can use the filter "jetpack_get_available_modules"