This is so much self-righteous crap. Obviously this is (a) about hating on the white south, and (b) feeling good about doing so. Dean Hall is, from what I can tell, another aging boomer; he's a Californian with the most impeccable progressivist credentials (went to EDS and served at All Saints Pasadena). He seems to be utterly clueless about white supremacists other than what he reads on the Southern Poverty Law Center, failing to recognize that his Yankee interloper stance helps justify their cause.
Look, he as much as admits that the window is, in its way, about reconciliation. Lee and Jackson were once hugely admired figures even outside the south. I personally, being the son of a man who left Charlotte NC with every intent of never returning, and having survived the Dukes of Hazzard period, take the "Stars and Bars" as a useful indicator of people who aspire to be southern hicks. I have no love for the banner, and no great love for southern culture; I won't live south of the Potomac, and my Ohio-born mother frequently found Maryland too far south for her. But the current, abrupt reaction to treat the battle flag with the same hatred as is directed at the Nazi flag is contrived and repugnant. It is now, in this hatred, a symbol of progressive hubris, and a sign of rejection of the gospel.
The current battle flag animus is not really about blacks at all. It's about making progressives feel good about themselves in spite of the fact that they can't do squat about the problems of poor blacks, and don't care squat about poor whites (who, after all, are racists through and through and therefore deserve to be hated). Taking out a window (and sticking in something about slavery instead) perhaps makes the cathedral a better House of Prayer For All Upper Middle Class People, but it also acts out every crazy right wing theory about self-hating white liberals.
I'm presuming that there will be enough backlash from cathedral donors that this asinine effacement isn't going to be carried out; and perhaps the whole point is for the dean to curry favor from his fellow progressives for Speaking Truth to Power (and never mind that he is the power here). In any case, I utterly oppose this.