I'm not sure exactly what you're asking, but if it's what I think it is, you may need to set the search base to something closer to the root of the tree.
Eg, if you have the base set to something like:
ou=Department1,dc=company,dc=com,o=internet
ou=Department1,o=companyname,c=us
Try stripping off the ou:
dc=company,dc=com,o=internet
o=companyname,c=us
You'll also need to make sure the search scope is sub
not one
.
The only problem comes up when the uid (or whatever you're using as the login) isn't unique across departments; I'm not sure how you'd handle that. (I assume it's possible, as I know I log into some systems using 'realm/user', I just don't know how you'd map that to something for 'AuthLDAPURL', that you'd be using in this case)
For a breakdown of forming an AuthLDAPURL, see Subversion with Apache and LDAP: Updated or RFC2255