This is a really exciting problem space, and I feel some envy at the thought of your task :)
I haven't worked with Quark, but years ago I did something similar working with Indesign. We needed to produce education resources at a fast pace, including work from many contributors into a single document, with editing phases as well.
I started thinking that Indesign was the centre of the system. But I had to change to a mindset where the backbone of the system was a chain of tools. Indesign was just one tool plugged into that system, focused on doing the things it was good at.
Building it this way, I was able to deal with textual issues in a different part of the toolchain, and had complete flexibility about what languages I could use to do it. (i.e. not stuck with applescript)
Here's an example for how this flow could work involving quark:
* Your users create their source material in whatever format. Some will give you word, others smile, others text.
* Consolidation phase. Consolidate the bulk of your content into a single place.
You could abuse quark for this purpose, but if you
do: completely ignore layout concerns. The purpose of
this phase is to get all your content (images, text)
in a single place, associated with one another.
Then you'd export to XML. Again: no layout in
this phase.
* Review phases. Here, use your textual tools to work with the text. Get all the content right.
* Layout phase. Now quark, and layout. Feed your completed text into quark, and arrange it.
If new content arrives, have a mechanism so you can feed it straight into the review layer, and then into quark for re-layout.
> My goal is to script the editorial style guide of
> the magazine I work for, thus side-stepping a lot of
> formatting/spell checking that we do, so I can focus
> on fact checking.
If you were to break it up like I mentioned above, you could even have different phases from fact checking and regionalisation. And you could see your data flow through the stages, and have diffs available to supply to interested parties, such as the content author. This allows you to add powerful new kinds of markup that doesn't need to appear in the final document. For example, XML markups for fact-checking events, "<check time="20130527-1225" person="joe">Confirmed with call to witness, see full writeup at [blah].</check>".
You wouldn't be doomed to an existence of XML editing to do this - you might have a tool sitting on top of it. But to get it going you could just edit the XML manually.
There's other advantages.
Say you wanted to publish to web and and to paper and to braille all off the same content. No problem. Just take your textually-correct document layer, and pass it to the braille processor or the web processor. You'll get exactly the same content as went into the paper published version.
You could feed that layer into a datastore and run a textual search program against it.
Or you might want to publish a single volume of all of the year's content, with a single index. Again, it becomes straightforward.
Now you control the text.
If you want to discuss in more detail, feel free to contact me offline.