...well, I see 3 ways:
a) change weights. If you change weight for some item to 0, it never spawn until you direct place that on map
b) for special levels - reusing existent: may be try iterate all items on map and delete/replace unwanted item? If it is not a reward from Agony Elemental or Arena Master but just ordinary item on level like envirosuit or large med-pack. At OnEnter event
c) in documentation I see a level.OnCreate(being/item) event. Looks like place to control everything including special rewards like sculls-Arena staff-lava element ?