Here's an idea:

Cure - upgrades to Afflatus Solace when in possession of a Lily (similar to BLM's Blizzard/Fire upgrading to Paradox when in possession of a Paradox marker), Freecure made into a trait that allows any Cure spell (including Cure II/Cure III) to grant Freecure.

Physick - upgrades to Leeches (Esuna + low potency healing spell).

Benefic - directly upgrades to Benefic II (AST has the best low-level MP management anyways), Enhanced Benefic trait removed.

Diagnosis - unchanged.