Probably not the best way, but one workaround for this task would be to Freeze the document that was checked out. When Alfresco queries you for the reason of the hold, you can type in "Checked out by John Doe" or some other boiler plate text that your staff agrees on. The audit trail metadata will track the text you enter and if you do any cutoffs or deaccessioning, you should get a warning about a 'frozen' record that you'll need to deal with i.e. get the record returned by John Doe before carrying on with your activity.
Ideally, what should probably occur is an additional metadata field that could be activated only for non-electronic documents. The field can only contain the alfresco username of the user who checked out the document. A nice to have addition a custom query that shows documents that have on loan for more than X number of weeks so as to allow staff to remind borrowers to return the record to the repository.