No; throttling can (and is, in many cases) applied to any traffic that passes through, regardless of what it is.
Also, encryption doesn't completely hide the nature of the BitTorrent protocol. BT has several unique traits, namely a lot of connections on a single port, or a small bank of ports, not to mention traffic flowing both ways followed by traffic suddenly becoming all outgoing when the person becomes a seeder. This is the big thing, and this is what triggers "solutions" like SandVine to start sending RSTs to disrupt traffic -- right when it sees you go from downloading and uploading on a port to simply uploading, it tries to shut you down.
I don't even need to go into why this is far less ethical than your average individual's use of P2P networks. Companies like Comcast, Cox, Rogers, etc, choose to ignore the numerous legal uses of BitTorrent. BT has the potential to save free projects thousands of dollars of bandwidth fees. Many Linux distributions actually rely on having seeded torrents because they cannot afford hosting out-of-pocket for free projects (when distributions get larger, of course, things change, but my point still stands -- Gentoo, Fedora, Ubuntu, and many of the other major distributions encourage BitTorrent use).
I swear, the Democrats had better get elected and they'd better fucking support net neutrality. Especially Obama; if he gets into and doesn't start lobbying for it I'm going to be highly pissed off.
