Olympus E-Pl1 Remote Flash - How do I avoid the on-camera flash impacting the photo?

I'm not sure it's possible to limit the 'PL1 on-camera flash to only send out the control flash bursts, but you might try either simply using a small piece of white cardboard at an angle to block the light to the subject while still allowing light to hit the external flash, or using a piece of exposed film to act as a filter that will allow infrared light to hit the external flash's sensor, but won't let any visible light through.