The statement occurs around 2:50, as linked here.
He also says that the Emanuel African Methodist Episcopal Church, in particular, has been "viciously attacked many times", but I can't find any other instance of it being attacked except once in the 1820s after a slave revolt, about 150 years ago.
Is he just lying?
He is certainly not lying. The civil rights movement was also lead by religious leaders as you certainly know, thus their churches were an obvious place to attack their efforts.
One famous incident was the Birmingham Campaign children's march, when children and youths were attacked by police after they started their peaceful demonstration from 16th Street Baptist Church in Birmingham, Alabama. So it was not a direct attack on the building but on the congregation: