Ultimately, here's what we will enact as house rules in my games:

1) Sorcerer Square no longer sells spells. However, it has a resident alchemist there, so that other players have easy access to gold. This alchemist also has the ability to turn magic objects into three gold.

2) Magic Emporium no longer sells scrolls. It sells spells instead.

This keeps the Alchemist's abilities the same while eliminating what appears to be a rather glaring loophole in the game's design.

I've elimated the spell book and flail, the scribe is a one shot and discard deal like they did in DE, you can buy spells at the sorcerer but not sell them (this removes the ability for the warlock and such to gain three gold every trip through the city), and the simplest fix for the alchemist is really just having a standing rule that purchased goods are alchemized for one gold whether they are magic or not. I think giving everyone the ability to turn in magic objects for three gold robs the alchemist of a key ability, maybe it would be fine until someone played the alchemist though but I'm not trying to make gold any easier to acquire than the highlands already has.