I've been watching your efforts to have this kind of "self-contained" JMS service for a while and I strongly feel like you're making things way harder than they need to be. If your service starts up ActiveMQ fresh when it starts, and shuts it down when it stops, then why does it have to clean up queues? If you're using an existing ActiveMQ instance then is leaving the queues up for reach of your services really a burden? I don't see the practicality of what you're doing outweighing the effort you're making to do it.
Anyway. In answer to your question, there's no "official" way to manually clean up the background subscriber/connection assets being used by a messaging VSM. There is, however, a script you can run to clean up *all* background connection assets:
testExec.getStateObject("lisa.hidden.assetstate").destroy(testExec);
This should clean up all the background subscriber/connection assets immediately in most cases.