It all depends on how deeply the rust has pitted the metal.
If the rust has pitted very badly, then it might be detrimental to the belt unless the rust scale is buffed away thoroughly before running the deck. A wire wheel in a drill, or remove the pulley and use wire wheel in a bench grinder to buff away the rust scale.
If you are replacing a "like for like" deck.............what is the condition of your old pulleys?
If your old pulleys are good....swap them out for the rusted ones.
If the rust you see is nothing more than a little "surface discoloration" just go ahead and run the deck.
You might even want to run the deck with the OLD belt (if usable) for 1 mowing before putting on the new belt (presuming you were going back with a new belt).

Thanks Mowie. I think I will run the wire wheel brush.