It IS accepted as fact by everyone but basically right-wing Japanese historians and politicians, sort of how the Rape of Nanking is accepted as fact by everyone but such right wing Japanese groups who propagate the same propaganda used by the fascistic Japanese government of World War II.

The New York Times article's point (if we're talking about the same article) was not that OMG, this thing we've thought was true for decades, might actually not be. The point was that this represents a prominent point of contention that reflects the current state of Japanese politics. It is also a growing point of contention among Japan, Korea, and China, with Korea and China being still very actively bitter about Japanese actions in World War II and earlier. The growing importance of Korean economic power has led to there being several statues built in the US commemorating Comfort Women, and the adding into some US high school textbooks in Virginia information about Comfort Women.