One way to approach this is let your security model work for you. If you make Drafts in each Department Home readable only by individuals within that department that are working on those drafts, then doing a search of all documents will only return ones that you have permission to read. If you belong to that department, then you might get the Drafts contents as well.
Another approach is to create an aspect intended for published documents – this is a good idea anyway. The aspect might include publication date, expiration date, and status. The status of DRAFT would indicate that it is not available for general searching, or PUBLISHED would indicate that it is. Then, extend your Lucene search with a check for having this aspect, and the aspect status having the required value.
