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You could require content approval and turn on track changes. (In Word 2013, you can require a password to turn off track changes.) Then the person who has to approve the document can accept or reject individual changes once the document comes to them. Or, there's a "collect feedback" workflow that will route a document for comments.
You could make a separate list (i'd use a discussion board) that ties to the document library through a lookup column to allow users to make comments/questions on a specific document. This separates the concerns of users having access to edit documents that they don't need to edit.
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