Well, in a case like that. I likely wouldn't upgrade Wordpress immediately unless it were a bug for a serious security exploit or something that they fixed. I'm pretty cautious about applying software upgrades willy-nilly in that regard. But I certainly understand by your own personal experience, why you would place a heavy emphasis on cautioning your customers.
If I were in a situation where I needed to update WP and the plugin either didn't have time to, or couldn't catch up, I'd more than likely just disable it for the time being, and set up a temporary unprotected links page to make due.
In other news, after exploring some more of wpfilebase's options, it really is quite extensive. I can set individual or multiple files up for access to different user levels from Admin, all the way down to Subscriber, and in an emergency I can set files to admin access only. So, it looks like the plugin can do quite a lot, including "members only" type content, if I decide to switch to that model. I also created a test account and it does not appear to expose anything via the Dashboard.
So here's to hoping it doesn't fall by the wayside anytime soon.
I may be a bit combative, but I do appreciate the discussion.