You can assign different materials to your emitter and your particles. Unfortunately, making an object completely transparent seems to cause Octane to randomly reassign my visible materials the next time I reopen the scene. I was able to remove an emitter from a boids simulation by baking the particles and then deleting the geometry of the emitter in edit mode. However, this doesn't seem to work with other (non-boids) particles. Deleting the geometry -even after baking- repositions the particles.
Windows 8.1 64, 32GB, i7-4770K, MSI GTX 770 4GB