It sounds like they removed the historic relics/art from the church for the 'renovation' and then it was burned down.
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White hats burned it down to expose the dungeons of horrors (Donnie Darko Style)
or
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Black hats burned it down to get rid of evidence (9/11 style) and/or destroy a national/religious land mark.
Either way, it's a message. It's pretty telling that POTUS is suggesting how to put it out (duh.) and that they let it burn…