If the pump has an anti-suck back valve simply turn the pump off. If
the system is supposed to be maintained at a vacuum pressure then a main
system valve needs to be incorporated into system design.
If the pump does not have an anti-suck back valve then the pump inlet
should be vented to atmospheric pressure before or immediately after the
pump is turned off. This equalizes the pump inlet to ambient
pressure. These valves can also be automated so that the system can
be maintained at pressure.
These pumps can be run 24 hours a day with no real ill effects, they
are designed that way, and as long as there is oil in the pump then the
can be considered for continuous duty.
It is good to document a shutdown procedure that gets a little complicated
and mount it somewhere on the pump so the uneducated, unknowing can follow
in your footsteps and not blow off a whole bunch of material by
contaminating it or the like, remember Mr. Murphy?