Perhaps not call the app TextSecure then? I think Moxie is a total dude but wasn't SMS encryption the Unique Selling Point of TextSecure? It was the reason I installed the app and go through the inconvenience of typing a very long string into the app every time the app restarts. I undertsand the logic of what Moxie is saying, if that's the case then the conclusion should be, "We need to shut down the entire app", not…
The reasons make sense - SMS as a transport is almost unworkable, there's a lot of crap involved with MMS bugs that it would be good to rip out, and it can never be compatible with iOS.
A replacement for GCM/push/etc for wakeup would be nice - I wonder what that would look like? - but it'll do for now.