Perhaps he is glad that the architecture and art of this shrine are telling pilgrims in no uncertain terms, "Go away! Stay far away! This is no longer Catholic here." The design is giving visual evidence of the loss of faith.
You've absolutely summed it up! And what a shame, I've always wanted to visit San Giovanni Rotondo. I guess I still could, and just stay clear of this 'shrine'. Pity, though, the misguided who visit the shrine and think it wonderful.
To get a feel for what Rauschenberg's rejected stained glass windows might have looked like, here is one of his pop art collages created expressly for a monastery in Venice...
Sadly, the monastery probably proudly displays it, in all it's ugliness. To me, it looks like a bomb dropped somewhere and this is the immediate aftermath. How awe-inspiring and faith-filled (sarcasm).