I don't think you necessarily need to upgrade I's to II's, though I's are redundant at higher levels.
I think Benefic I to II does make sense, because AST has other healing skills and MP recovery at that stage anyway. I mean I actually don't have Benefic I on my hotbars anyway. So yeah, II should replace I when you learn it.
WHM is a little different, as you said when it gets Cure II, those are their only healing skills for a few levels, plus WHM doesn't have many skills as it is. I think WHM could legitimately keep Cure I, but the freecure effect has to change. Instead of I proccing II, have it the other way around. A Cure II has a chance at increasing the potency of a Cure I, so that you get a Cure I that's just as potent as Cure II, but for a lower MP cost.
Physick should get an upgraded effect that coordinates with the Faerie. Maybe using Physick automatically causes the Faerie to use Embrace on that target, regardless of it's normal priority system, essentially upgrading it to 550 potency.
