Late though it may be, I'd like to offer my thoughts, looking at things through a coding/ RAWs logic lens.
Herbs; There are/would be a specific set of capabilities for herbs, and a means by which it would have to be applied.
[CURE_RAW:(cure)
#)] - The raw herb must be applied.
[CURE_EXTRACT:(extract):(cure)
#)] - An extract from the plant provides the cure.
The # relates to effectiveness. In the future, additions such as [CURE_SMOKE] or [CURE_COMBO] might be added.
For the (cure) fields;
BLEED - Helps slow/stop bleeding.
PAIN - Helps reduce/eliminate pain.
INSANITY - Helps reduce/eliminate mental shock.
POISON - Helps against most poisons.
POISON:(poison) - Helps against a specific poison (see: antivenoms)
Other effects for problems such as necrosis/gangrene could be added.
Surgery; A Doctor profession would work, but would need or at least highly benefit from a Medicine tab in the Status screen. Such a tab could handle assigning treatments, checking on dwarves' injury status and perhaps control of practices/policies such as "give painkillers freely/restricted/never" to exert more control and allow us to preserve resources (i.e. if you don't want the doctors to accidentally use your Golden Apples on a miner when you want to keep it on hand for the legendary axedwarf)
Making hospital beds a sort of workshop might be a way to allow control/involvement beyond "throw doctors at it"; the Medicine screen could indicate what treatments are needed, and you would make judgment calls on what needs to come first (i.e. keep them from choking on their own blood first, THEN set the broken legs and sew up their face). This would also make it easier to integrate each treatment type as a job for the purposes of handling resources/fitting into the existing labor paradigm, and would easily allow check-ups to be queued.
Prostheses; Leave this to some kind of noble that is attracted based on your fort's medical prowess or the availibility of something worthy of his interest, such as a rare medical herb or live captures of a rare creature. That way, it's not dissapointingly common, and isn't guaranteed, plus it gives you new goals.