We are using BuddyPress Group Hierarchy plugin which may provide the flexibility you are looking for.

http://www.generalthreat.com/projects/buddypress-group-hierarchy/

It allows us to create major topic groups and have subgroups beneath them.

http://facultycommons.txstate.edu/groups/

Custom CSS option which worked for us to hide the WP logo and popup without hiding the entire bar was:

li#wp-admin-bar-wp-logo.menupop {
display: none;
}

I was having similar issues in a mac environment using firefox. Switched to safari and was able to make changes.

Thank you Scott. Not the answer I was hoping for, but what I suspected. The categorization of the wiki at CUNY Academic Commons was actually one of the features we were looking for. But maybe it won’t be as big an issue as we think.