Ya! leave it alone. It should clear up soon!. Could add extra pump/
pH for more circulation which should aid in survival of creatures (many sleepless night with IR/flashlight trying to see what's there) on the rocks. Change the direction of flow from time to time to make sure there are less dead zone.
Some people will use mechanical filter media to have water clear up but this can remove good amount of microfauna which is needed to achieve well balanced MINIREEF.
Add carbon in fltration if desired to lessen the odor. May need truckful loads depending on the condition of rocks received. LOL