the function that you request is not currently available via web-service.
As you say it is only possible to delete a document (and therefore all its versions).
In the upcoming 7.6.3 version there will be an expansion of the functionalities available via web-service to manage the following aspects: tags, bookmarks, ratings, notes on documents
Of course we can implement the functionality you requested and I think it will be a good addition,
so I suggest you fill-out a feature request on our issue tracker http://issues.logicaldoc.com/