I think Trump hired Bannon primarily because the latter knows a fair bit about propaganda and catchy headlines. Counselor to the President isn't a very public or powerful position, unless you think somehow he's going to manipulate Trump into thinking "You know what, maybe we should bring back segregation". I mean, Trump's a dummy, but even if Bannon somehow got Trump 100% on board with his views, the moment Trump's Twitter feed starts exploding and his approval rate plummets, he flip-flops, fires Bannon, and takes a selfie with some random black person to show his commitment to racial equality or whatever. Until that happens, this is just a continuation of the usual fear-mongering that occurs whenever any candidate outside of the mainstream gets endorsed by extremist group X.
I will admit that Trump's rhetoric inspires particularly stupid individuals on the alt-right to commit violence, and we'll probably see more Dylan Roofs coming out of the woodwork during Trump's presidency, so it will be up to him to very loudly denounce it if/when it happens.