Just from reading your post, and not actually trialling anything here, can't you do like you suggest and set the rating to not be stored in the file, and then get the auto-import feature to take care of everything else?
The only point where I can see this approach falling over is, if, for example, you use your (presumably the main) library for "managing major structure changes" and rely on auto-import to keep the second library up to speed, you may find the "fix or remove broken links" erm, feature, gets a little slap-happy, removing files from the database and re-importing them from their new location as totally new files, rather than fixing the 'broken links'. This would obviously result in the loss of not only ratings, but any other database only info such as [date imported], [number plays], [last played] etc. etc.
How often do you do "major structure changes"? Having settled upon a file naming template I'm happy with, I've not done any major restructuring work for years. Back in the day, I do remember chopping and changing things quite a bit, but realised that stability and continuity in this area is a pretty fundamental requirement for managing a large-ish library, at least for my mind anyway. I quickly worked out something sensible that worked for me and stuck with it, it's never hindered me, and I've never looked back.
Incoming music, be it ripped or downloaded, all lands in one central directory for previewing and tag checking, and once that's done, MC's rename from props tool is used to move the files over to the media drive beside the rest of my audio. Auto-import does not watch the main audio drive, only the incoming directory.
If you were able to adopt a similar workflow, so that once files arrived in their final resting place, that's where they'd stay, you could pretty reasonably use your own library for managing the media, and set the secondary library to watch the main resting place for any new files you placed there. Depending on your own particular environment, and whether or not it could adapt to that kind of scenario, and how you arrange/educate the other user(s), the theory feels sound enough for a test run.
As for library corruption, you shouldn't need to worry about that if you make regular library backups, something which MC also does automagically. So, you can rely on those, or make your own scheduled backups using dedicated backup software.
FWIW, I only store [artist], [album], [name], [date], and [comment] in my file tags, trusting the rest to the library, and find MC to be a lot nippier as a result.
All of that is only a suggestion, because I believe, that as things are at the moment, everything else you asked about falls under the heading of "Feature Request" and as such, could potentially take a while to be realised, if at all.
regards,
-marko.