I just created two different wikis:
gollum --page-file-dir wiki1 my_repos
(Control-c to stop running gollum)
gollum --page-file-dir wiki2 my_repos
I created a home.mediawiki
file as the homepage for each. So they are occupying two different namespaces.
To edit these at the same time, I suppose I'd learn to use a different port for the second instance of gollum, or just commit notes to one directory or the other (wiki1 or wiki2) through my text editor, which is probably what I'll be doing anyway.
Since wiki1 and wiki2 are directories on a computer with a GUI interface, I'd just use Finder/Windows Explorer/whatever to maintain the list of them.
Does that meet your needs?