Since you are transferring it and the rock is not sitting in an established tank, you do have some options. I don't feel manually removing it will be successful in the long term unless you QT and observe for months to make sure no vermatids survived. Even if one makes it then you will have more. You could put it in a tub and treat with a low dose of copper and observe. That should kill ALL inverts/corals/sponges on the live rock, but not the bacteria. If low enough dosage then the coralline will also survive. LR does absorb copper so you will have to run different agents to completely remove it from the rock before you add inverts/corals/sponges. There are threads on here with people treating their DT with copper at levels to kill parasites, then a few months later adding corals and inverts. Making sure the majority of the copper is out of the rocks is always key. Instead of using copper there might be other medication you can use that will wipe out all the inverts without affecting the bacteria and coralline, but I am not aware of them.
Keep in mind killing a lot of inverts will cause ammonia. You know what, why couldn't you dose ammonia? That will still kill all the inverts/corals/sponges but should not affect the beneficial bacteria. No idea what it would do to the coralline.
Might be able to mix up a potent coral dip and let the live rock sit in it. Most dips for corals will not kill vermatids easily, but if the LR is sitting in it for a few days then it might kill them as they exchange internal/external water.
Whatever you do it will have to be relatively extreme to make sure no vermatids make it to the new tank.
This thread has my creative juices flowing. I am almost tempted to pull a piece of LR out of my system and start experimenting on it.
