It depends on two things.
Firstly, whether we see the Catholic Church as a person (personification) (then nobody would fit) or as an institution (the nothing fits).
Normally, we have no problem with institutions just being objects:
That is the hospital that was in the news last night. (not who was in the news)
That is the school that refused to let the inspector in. (not who refused)
When we name the institution, we can personify it, but only if "it" performs an action.
St.Anna's Hospital, who opposed new regulations...
St.John's School, who refused the inspector...
The Catholic Church, who claimed the Turin shroud was real.
These are all more or less acceptable, but some (most?) people may prefer to use that instead.
When the institution does not perform the action, we certainly never use who:
St.Anna's Hospital, that was in the news (not who)
St.John's School, that was investigated (not who)
The Catholic Church, that was claimed to have embezzled money (not who)
Here, the author has chosen to not personify the Catholic Church.
Secondly, the author alludes to a number of causes for the eradication of history, and that groups certainly won't consist only of concepts that can be personified. There could be fires, storms, earthquakes...
By writing nobody has done more..., the writer would tell us that only people are responsible for the eradication of that history. He has chosen not to limit himself to that, basically telling us that the Catholic Church has not only done more than any one else, but more than anything else, including natural disasters or time itself.