Unfortunately, at this point, if you delete the voicemail from the app, it doesn't take it off the voicemail system. I consider this to be a design flaw. You should be able to remove the message from your voicemail from within the application.

On the plus side, if you log on to your account on their website (where you can also look at all of your messages) and mark a message as "read" it removes it from the voicemail system. To save time, I find it much faster to go online every so often and mark all the voicemails as "read" than to dial in to my voicemail and delete each one individually.

I hope their plan is to fix this with the final release.