Officially, you should go to the admin console and delete the users you want using that tool.
Unofficially, the only way of deleting all those users in a single action would be to write a SQL query against the jiveUser table. I'm pretty sure that would work (as long as you didn't delete your admin user), but no guarantees.
Ok, I'm curious then, what is the point of the "LDAP integration"? It seems ridiculous that it will pull user information from the directory, but never again update the information with the information in the directory. Or, is it just not updating because I changed the base DN? If I left the base DN the same, and modified a user in AD, would it update then? It seems that the ability to pull users from LDAP, then never deal with LDAP again is kind of silly.
Also, bulk modify, delete, etc, should really be written into the software. I'll do it with SQL queries now, but I can't imagine that it wouldn't be key for the product.