Removing aluminum foil barrier/insulation backer in new hot roof
The purpose of the foil was as a radiate heat barrier and may have also held the original insulation in place. Now that you have insulated with close cell foam I do not see any problem with removing the foil. Like you mentioned you can get rid of the rodent leavings and reduce places where they can live and breed plus places where insects can also live. I would definitely fix the booby trap pitfall it sounds like a big safety concern.