But potentially you have some options (might not be worth it though and just changing your queries is probably a lot easier.
What we usually do is setup multiple instance:
You can setup WD for a cluster 1 (primary no prefix) federating to cluster 2 (with prefix) for main cluster 1 users
Then the reverse for the cluster 2 users. WD with cluster 2 (primary no prefix) federating to cluster 1 (with prefix).
That does not use a prefix but it requires the database to be manually mapped to avoid conflicts.
Patrick