Wordpress Directory - Does it work on individual sites in MU

Before I install, I just want to check if this will work.

Can I use the Wordpress Directory plugin more than once in my MU set-up?

maindomain.com/directory1/ <- install here as niche directory 1
maindomain.com/directory2/ <- and install here as an independent niche directory

I was thinking that if I do not 'network activate' but, rather; activate on a 'per site' basis. Will it work that way?

Martin