I do something similar but use Advanced Web Ranking, use site:www.domain.com as your phrase, run it to retrieve 1000 results and generate a Top Site Report in Excel to get the indexed list.
Also remember that you can do it on sub-directories (or partial URL paths) as a way to get more than 1000 pages from the site. In general I run it once with site:www.domain.com, then identify the most frequent sub-directories, and add those as additional phrases to the project and run a second time, i.e.: site:www.domain.com site:www.domain.com/dir1 site:www.domain.com/dir2 etc.
Still not definitive, but think it does give indication of where value is.
