I did find a way to make it work. First install bbPress without WordPress integration. Next go to the bbPress settings and configure the WordPress Integration. Where it asks for the AUTH_SALT, copy the SECRET_SALT. Finally update bb-config.php with your wpmu specific defines.
I’m having the same problem and haven’t been able to work around it. bbPress did successfully install without WordPress integration. So, now I’m trying to do the integration manually.