The women of the UDC were unsuccessful in getting an Aunt Jemina style monument in Washington, D. C. to celebrate the loyalty of black women in being slave mammies, so they started lobbying for windows honoring two of the military leaders of the Confederacy as spiritual leaders. The windows were installed in 1953, just before the momentous Brown v. Board of Education decision of 1954.
I don't know that we need to continue to honor that tradition of reinforcing Confederate concepts of white supremacy in the National Cathedral, where state funerals of presidents and all kinds of national prayer events are held. The Dean has no specific proposals, but I believe suggestions have been made to remove and then feature the windows in an historical exhibit, but not to continue to hold up 2 Confederate leaders whose foremost mission was the ongoing enslavement of others as "exemplary Christian gentlemen." I would agree with the Dean.
We have to remember a stained glass window is not a history book. What it depicts is what the church at the current time believes is important to see or emulate.
While it is true that in the south in the 1860s slavery was not considered to be against the teachings of Jesus, such a view is not common today, and the church of today probably does not want to portray the value of fighting for an entity dedicated to preserving slavery as something worthwhile. Here we're talking about what is acceptable today, not what was acceptable in the 1860s.
This is a decision for the church to make based on what they believe are values people today should emulate.