Nope, there is no way to automate your milling, its just plain old dirty work. Here is what I do to make it go as fast as possible. Turn on auto loot, if it is not already enabled in your interface options and key-bind mill. Press you mill button and click a stack of herbs, once your GCD has expired press mill again, this should "blue" your pointer. once the mill cast has ended, click a different stack of herbs.

The goal is to get your pointer "blue" before the loot window opens to avoid the "you are busy looting error". Also while the loot window is open the herb stack will be grayed out and not available for further milling, which is why you need to select a different stack.

This method will keep your milling cast up with very little downtime. Have fun... just kidding milling is never fun.

Two more tips for milling; YMMV. Use Enchantrix and the auto disenchant option which will pop up a window asking if you want to mill herbs whenever a 5-stack (or combination thereof) of herbs shows up in your bags. Use Panda which offers not only a simple click interface for milling / crafting but also a general mill-the-first-5-herbs-you-can-find one-click button. Both will still involve multiple rounds of clicking to grind down your stacks of herbs. But they reduce the action to a single click per round of milling and limit the inventory hunting required.

Panda user here, but some of my addons are not auto-looting correctly and its weird.
Also, if you have a stack of 4 or less before a stack of more herbs, it will give you an error saying you need more than 5 herbs to mill. You just have to rearrange your stack so that all of the full stacks come before the one that has less. Same thing with a stack of 2 and a separate stack of three, you need to combine them to one-click mill them in Panda.

Apart from those issues, Panda is great for milling, de-ing, or prospecting.

I do not think what you describe is the way 99% of the high volume glyph creaters operate. Or at least the scribes that put up most of the thousands of glyphs on the AH.

They do not buy the correct level herbs, they buy the best value and let Jessica fix it

They do not buy in multiple of 5. They buy when the price is right. You post 4 icethorn cheap now it will go ASAP. And they tend to buy in bulk. A moderate glypher might need dozens of stacks a day. And supply is volatile so you buy it up when you can. Over the course of a few days you accumulate herbs. Then you spend some time in an extended milling, then converting pigments to ink, and crafting session.

So the scribe is doing #1 & #2 independent of this addon and prior to making the glyph decision.

But this is a non issue since the glyph market as we know it is going away, with a slight blip for Dec 7 goblin/worgen and some new glyphs.