I’m not suggesting a proprietary system:
apply_filters( 'themeblvd_js_locals', $locals ) is precisely what I had in mind for you to pass the booleans for various script support into
themeblvd.js. Then you just add conditional checks within that file for each section of code that deals with a particular feature (prettyphoto, superfish, etc). This is perfectly in keeping with WP standards, and a simple comment line before each section’s conditional test would be sufficient to explain to anyone tinkering under the hood what’s going on.
In fact, just by adding the conditionals to
themeblvd.js, even before you modified your global config, you would allow users to disable JS components by passing the localized variables themselves (in combination with manually dequeueing the scripts). This could be a quick intermediate step towards a more comprehensive global config system that would do it all for you – while being fully forward-compatible with those changes once they appeared (as they would be using the same mechanism)
[personal confession] I’m speaking as a previous Thesis power-user, where there’s either a hook, filter, or an options panel to override practically everything without ever touching or replacing the “parent” theme files. This has made it possible for me to safely update the core theme many times without ever worrying about whether my customizations will survive – or whether I’ve managed to find every last bit of new and improved “parent” code to transfer into my custom files.