What Roof did was truly despicable. Nobody will be turned away from a church, and he knew that. It is an example of the work of a twisted, sick individual who is in no way representative of anyone at all. If you want to use what he did to promote segregation, then you shouldn't be opposed to other people excluding others for similar crimes. For example, in light of many terrorist attacks, should people then exclude Muslims from certain events? Personally, I don't think so. These disasters are the work of terrorists who don't represent any functioning member of the general public at all. EDIT: With regards to your point about excluding people because they might take over the conversation; that's a fair point that I'll need to think over. I had a conversation with Herunar a little way down there who made the same point. At the moment however, I am unconvinced that the good outweighs the bad in the idea of self-segregation.
My point is that there is a lack of trust among many black Americans about white people entering their spaces. The church shooting crystalized that distrust among a lot of black people I know. I'm not sure how to explain the categorical difference between a group of black activists excluding whites versus a government or company excluding Muslims from an airplane. Well, one difference is de jure discrimination versus de facto, but even that is not what I'm getting at. Additionally, the message from a lot of the Black Lives Matter groups has been to encourage white people to form their own auxillary groups to support BLM.