I don't usually read Jezebel, but this is an interesting piece. My English teacher when I read To Kill A Mockingbird always maintained that Atticus was a genteel racist, and it seems she was right.
I don't feel qualified to argue with the article's author, and I haven't read Watchman (and haven't decided yet if I will), but couldn't you argue that Atticus is admirable exactly for the reasons the article is citing as flaws? A product of 'Southern genteel racism', he puts his life at risk for a cause he understands is all but lost from the outset. After all, Atticus understands the white people of Maycomb and at no point could you argue that he was acting under any illusion that the town would forgive him for arguing the defence of a black man accused of raping a white woman.
I need to go back and read Mockingbird more carefully, but I'm sure the author is right - I'm sure there is evidence of racism in Atticus. But there is courage, and a sense of justice, and something that transcends racism as well. How, exactly, do you quantify the worth of a racist who stands alone between the mob and the jail?