I would think if you repaired the vacuum pump diaphram, the repaired pump would suck most of the oil out of the system and back into the engine where it belongs. I'm not sure if there is any other way for oil to get in the vacuum system except through a failed vacuum pump diaphram?
Alternatively, you could disconnect each vacuum line that has oil at each end (rubber connectors) and suck some type of solvent through with a mighty vac. Once flushed out you would need to dry it out with compressed air.
Is the oil causing problems? Perhaps any problems you are seeing with vacuum is not due the oil, but due to an inoperable vacuum pump.
Good luck.
