Intellect is more than Theurgy, and the tax raid will use Int in entirely non-Theurgic ways (as the smuggling for Alaine already does). It doesn’t make you a great combat strategist, though - few intellectuals are. It incorporates book-smarts, memory, logic, and the ability to think quickly in the face of the unexpected.
You don’t automatically take a morale hit for being a Theurge. The priests’ feelings about you only start dragging down morale if you rub your outlaws’ faces in it by raiding temples…