Jetpack is based off a two-way communication between your server and the WordPress.com servers. That is done via xmlrpc.php. If you delete your xmlrpc.php file, some things will break -- for example, the initial sync for Related Posts, single sign on, the JSON API, Subscriptions, and a number of others that don't immediately come to mind (this is not an exhaustive list by any means). If you disconnect, you also won't be able to re-connect to WordPress.com unless the two way sync is re-enabled.
But it depends largely on how you're disabling xmlrpc. If you are simply deleting the xmlrpc.php file -- then yes, it will indeed break. This is a very bad idea.
If you are using the
add_filter('xmlrpc_enabled','__return_false'); method, then traditional WordPress XMLRPC will be disabled (so the mobile apps will cease to function, for example, as will a number of other third-party clients like Pressgram and IFTTT) but Jetpack will still function.
If you're filtering
xmlrpc_methods to remove the
pingback.ping method, then everything will still work, except for the pingback.ping method -- which really is the intended solution in the first place.