The wasteland had become a land abundant in greenery merely in the span of a few years after the Beast's fall. It was a result of especially high concentration of seithr. As the land is considered eerie and cursed, people usually stay far away from it.
The church was founded and created by Celica A. Mercury. She took care of Ragna, Jin and Saya. However, an incident happened at the church involving Yūki Terumi. After Saya gave Mucro Algesco: Yukianesa to Jin, the church was burned down and Celica was murdered. Ragna lost his arm and was left to die. Rachel Alucard, and later Jūbei, found him there.
In Ragna's storyline in BlazBlue: Continuum Shift, there is a flashback in which Jūbei apologizes, supposedly to Celica, saying, "I got [Ragna] involved after all. I'm sorry. I really am. You can hate me if ya want. I promised I'd never use it again, but… I'm just gonna borrow this one more time…". Jūbei is referring to the jacket and sword that Ragna uses, which were retrieved from the church by Jūbei and given to Ragna. They were kept by Celica following Bloodedge's disappearance.
There are numerous points in the storyline, in both BlazBlue: Calamity Trigger and BlazBlue: Continuum Shift, in which characters come back to look at the remains of the church. Jūbei, Rachel, and even Kokonoe herself have visited the site.