Are medicinal medications used to treat scabies safe?

Generally yes . Permethrin is very safe lindane can be problematic in young children malathione is generally safe.
Safety of scabies RX. The medication usually used for scabies is elimite(permethrin topical). According to epocrates which is a drug based app, the common reactions are burning, pruritus, erythema, and numbness/tingling. No serious reactions have been reported.