additional applications have to be manual additions, sorry
For me the
SME Site Maker Script makes it a piece of cake to install your app in /opt. You could use snoble's WP contrib, and then manually install WP in /opt/wordpress2 using the script. The thing that I really like about the script is that you can set the alias as well, so if you installed WP in /opt/wordpress2, you can access it at mysite.com/whatever instead of mysite.com/wordpress2...
I did install WP-MU on a test server yesterday. I haven't messed with trying to get subdomains to work (blog1.mysite.com instead of mysite.com/blog1), but it seemed like everything went fine.
Ryan