How about, whatever the menu structure for a given workshop (all displayed at level 1, or have to dig down, like Stone Crafts/Mugs/Instruments found beneath the initial heading of Stone things in a Craftsdwarf's Shop), as well as the option to add that job type to the queue, the ability to toggle off/on that particular job-type from creation by the aforementioned auto-job or manager screens.
I was going to suggest either some additional top-level menu item to list the currently toggled-offs, or appearing (scrollable) at the bottom of the maximum 10 items in the job menu (for selection so once can 'cancel the no-auto'), but you could leave it as a side character (or colour) in the existing menu systems indicating the auto-possibility state. It'd still be more convenient than it currently is, and not much worse than the whole Permitting of certain dwarfs/skill levels to use that workshop, something which you'd think should be closely related to the allowed jobs.
I do see some minor difficulty adding this functionality to the Jeweller's, though, with its slightly unique (if you'll excuse the split infinitive) job assignment menu. But as I rarely manager-queue gem-cutting/setting jobs I'd be content to let that one go. (Unless Ctrl-C and Ctrl-E toggles the Cut/Encrust auto-capability for each, where plain C and E actually adds said job. (If it is C and E, I forget, without loading up DF... and for that forgetfulness/unsureness I am truly ashamed...)