Harris doesn't deny labelling Islam, being in favour of racial profiling, or floating the idea of using nuclear bombs on Arab countries. Instead he attempts to justify. And Harris has this weird way of behaving that involves making stupid and obnoxious statements, such as using nuclear bombs, and then crying foul that anyone should take him at his word. Because he says it would be "terrible" somehow cancels out that he says it may be "necessary". It doesn't cancel it out.
Stigmatising religious groups is wrong. Racial profiling is wrong. Arguing for using nuclear weapons on civilians is wrong. Sam Harris said all these things. He is wrong. When someone is as far gone as Harris is I guess it would be near impossible to get him to realise his programme of stigmatising Muslims is harmful and has contributed to where we are right now.