I know I have also seen on JREF references to the museum connected with the shrine. That has to be the biggest propaganda factory around. If you compare it to the A-bomb museums, which are a bit one-sided, it just completely ignores the fact that non-Japanese died, were tortured, etc in the Japanese expansion conducted during what the Daily Yomiuri calls the 'Showa War', covering I beleive from 1937 to 1945. This would be another compelling reason to at leats remove the war criminals, never mind rewriting the exhibits in the museum.
The history of the shrine is a bit interesting, as McArthur orignally called for it to be razed, but compromised by having the governemnt give/sell it to a private organization, the same one that refuses to remove the war criminals from it now. And of course in turn, the government can truthfully state that they can't force the private organization to remove the same said war criminals because the government no longer 'owns' the shrine.