Atticus has been preaching to Scout about the importance of restraining her temper--and her fists--when she is faced with a situation in which someone antagonizes her with inflammatory talk. This time it's Jem's turn to face the music. Just as Scout failed to control her temper when her Cousin Francis deliberately tried to make her angry, Jem loses control completely after Mrs. Dubose insults Scout and accuses Atticus of "lawing for niggers." Jem probably figured his actions were just--destroying the things that Mrs. Dubose most loved--but Atticus thought differently.
"You can't hold her responsible for what she says and does... I'd rather she'd have said it to me than to either of you, but we can't always have our 'druthers."
Of course Atticus knew more about Mrs. Dubose's condition than he was willing to let on to his children at the moment. Aside from the fact that their neighbor was "old and ill," he was also trying to prepare his children for the gossip they would soon be hearing as the Tom Robinson trial grew nearer.
"... when summer comes, you'll have to keep your head about far worse things... maybe you'll look back on this with some compassion and some feeling that I didn't let you down."
To Atticus, it didn't matter that Mrs. Dubose was a sick old lady (or that she was trying to rid herself of her longtime morphine habit): He believed that his children always needed to control their tempers no matter who angered them, be it Cousin Francis, Cecil Jacobs, Mrs. Dubose or Bob Ewell.