I've seen that uninventorying a resource in RHQ takes about 10-15 seconds. For 1000 resources, that's around 4 hours. The performance is so bad it maxes out a couple of CPUs in Oracle, plus it's written to require the agent to uninventory as well while holding up a database transaction. In other words, you can add a thousand resources in under 10 seconds, but it's 4 hours to remove them all.
Naturally all I want is RHQ to flip a bit in the resource table to ignore the type. I could do that in a few seconds by SQL. But RHQ has to remove all the resources of that type, which can be a lot of them. By the point I uninventory them, they basically get rediscovered again. The disabling resource feature is then practically useless. It can't possibly uninventory everything in the 5-10 minutes the database transaction limits you to: https://bugzilla.redhat.com/show_bug.cgi?id=1041910
The better solution is then really to edit your plugin, remove the resource types not needed, then redeploy.