If jiraiya was stronger than itachi, why didnt he just wait in konoha for itachi and kisame to fight them alongside kakashi?
Considering Jiraiya was on a mission with Naruto to go get Tsunade, he can't exactly wait around for Akatsuki to come before he went out to find Tsunade, she was needed straight away to take the Hokage role.

Jiraiya took Naruto with him, because he knew the Akatsuki would strike but not exactly when, and he would be safer with Jiraiya than any other person, not many people actually liked Naruto, and Jiraiya being the strongest took him.