Atticus uses the term "disease" deliberately. A disease infects and spreads, which is what happens in Maycomb. Good people, kind people, are infected by the disease. The disease spreads throughout the town. Then, suddenly, those kind people are acting against their nature.
Take for example the incident at the courthouse. Having been infected by racism, a mob of men show up to lynch Tom. They are not acting rationally, they are infected with the mob mentality.
Atticus cures them of the disease by calling on their better nature. He asks Mr. Cunningham about Walter specifically, reminding him of what is important and what message he is sending his son.
The cure that breaks up the lynching does not hold up in court, unfortunately. Despite overwhelming proof of Tom's innocence, the town is too infected to act honestly and allows their racism to control their actions in their conviction of Tom.