I used to have to patch the JACK patch to make Mumble not auto-connect to the standard outputs. With JACK being officially supported in Mumble 1.3, that's no longer the case. Instead, you have to modify the config file by hand.

In ~/.config/Mumble/Mumble.conf:

It's a standard ini file, so look for a [jack] section. If one doesn't exist, create it:

[jack]
autoconnect=false

And you're good to go.