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It should certainly be possible to use Linux level access rights to control who can access a specific library. Whether the library will end up being hidden, or the user simply gets an error when trying to switch to it with insufficient rights (which I suspect is most likely) I am not sure.
You are going to have to be extremely careful in the mechanism you intend to use to stop multiple instances of Calibre running at the same time against the same library. If you get it wrong you could end up with inconsistencies between the metadata.db file for a given library and the eBook files it contains. However it may well be a workable stop-gap until Calibre is finally enhanced to allow multiple instances to run against the same database.
Note, also, if that something does go wrong and inconsistencies occur it should be possible to use the Calibre facility for rebuilding the metadata.db file for a given library from the ebooks files that are present in the library.
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