The “usual disease” is racism, and Atticus does not want his children to become racists.
After Scout’s altercation with Francis and dispute with Uncle Jack, she overhears Jack and Atticus talking about the trial. Atticus explains to Jack why he has chosen to defend Tom Robinson, even with the effects of the case on his family. He tells Jack he could not face his children if he didn’t, and taking the case is a way to avoid Maycomb’s usual disease of racism.
Why reasonable people go stark raving mad when anything involving a Negro comes up, is something I don't pretend to understand... I just hope that Jem and Scout come to me for their answers instead of listening to the town. I hope they trust me enough.... (ch 9)
Atticus has done well with his children. Neither of them is racist, and they have grown up knowing how to respect all people regardless of race or class. This is why Atticus took the case, because he knew the trial would tear the town apart, but he had to do what was right so his children could learn what was right themselves.