Illuminate new facts and reinterpret old facts to develop a more accurate and truthful understanding of what happened in East Asia between, say, the middle of the 19th century and the end of World War II? Fine. With a focus on Japan, China and the United States during the 1930s and 1940s? Fine. This is what historians and curators do. And there isn't a book or museum today that tells the story of those troubled times well.
But I would think that a shrine like Yasukuni is about spiritual, not intellectual, integrity. That Yasukuni has a museum at all -- no matter what story its exhibits presume to narrate -- would seem to compromise its integrity as a place where one might go to impartially pray for the repose of the souls of all war dead, including the vanquished the victors hanged as war criminals.