It seems to me like I'm asking a simple, obvious question: what is stopping governments from simply shutting down Bitcoin within their physical borders? You think they will not be smart enough to handle a simple port number change?
Regarding the comparison with Bittorrent, my ISP (Comcast) did in fact block and throttle Bittorrent, successfully, until someone sued them. It seem to me Bittorrent is an example of how ISP's can block an application, not an example of them being unable to do so.
"The client could probably just check periodically for a signed message from a central server (or a broadcast on the network itself) with instructions to currently operate on the network." -- why could the ISP not block this, also?
Especially if the software is open source, as Bitcoin is, all the knowledge of the inner workings of the protocol is public knowledge, which makes it impossible to stick in something like "just check periodically for a signed message from a central server (or a broadcast on the network itself) " secretly without governments wanting to block the system knowing about it.