Trump often trumpeted a false claim that churches were under attack by the IRS due to the Johnson Amendment.
"It is remarkable that this is happening at one of the country's best known cathedrals."
The Fundamentalist Church of Jesus Christ of Latter-day Saints is also fighting a lawsuit saying the church discriminates against nonmembers and denies them municipal services.
Police believe Roof killed nine at a African-American church.
The mosque, set up inside a former Catholic church, has prompted protests