I develop a plugin that also uses Backbone. I've never had a library collision related to backbone before, and the collision is my fault (I was concatenating several JS files and enqueuing as one file), but once I fix it on my end, I think there will still be a potential problem on your end.
In jetpack/modules/notes.php, when you guys are calling
wp_enqueue_script, you're specifying the script version as
JETPACK_NOTES__CACHE_BUSTER instead of the actual version of the script, where
JETPACK_NOTES__CACHE_BUSTER is defined as
JETPACK__VERSION . '-' . gmdate( 'oW' ).
Won't that create problems for everyone else trying to use backbone? Won't we be forced to support the same version of backbone that Jetpack supports? The same goes for underscore and possibly other scripts enqueued in that file.