Isn't this wording just a misunderstanding on the users' behalf? You download a messaging app, you want to message your friends, and it needs access to your contacts. I don't see this as being suspicious. In other apps such as a music player or photo viewer it may be suspicious, but a messaging app has a clear need to know who you can connect with, and I think Whisper Systems saying "We do not store your contacts..." should at least give them the benefit of the doubt (if that's not enough, you can always read the source or speak to Moxie yourself).
Seems like much ado about nothing.