Often vets will use human terms to describe the problem in a guinea pig witout realising how misleading this can be - many times i have heard people being told by the vet that their guinea pig has a cold - guinea pigs can;t get cold viruses - but they can get bacterial infections of both the upper (URI) and lower (LRI - pbeumonia) respiratory tract.
So just to clarify:
Scabies is a human disase caused by a burrowing mite that has a preference for humans not guinea pigs.
Guinea pigs can get a different type of burrowing mite which causes more severe symptoms and if not treated can cause baldness, severe skin sores, fitting and ultimately death. The correct name for this disease is sarcoptic mange or acariasis. This mite does not transfer to humans.
Guinea pigs can also get other types of mites (often called static lice to add to the confusion) which are less severe but need to be treated nevertheless as they cause irritation.
The treatment for both these conditions is ivermectin and in view of the fact that your vet clearly thinks it is the more severe of the two then injections (three in total - one every 7-10 days to break the mite life cycle) will be required instead of the topical spot-on treatments widely available.
Hope this helps
x