Not only Itachi did never want to fight leaf people, he was already exhausted to the point he had to deactivate his Sharingan. Itachi was in a position where he and Kisame were caught off guard by Jiraiya, while he wasn't even aiming at him but was busy with Sasuke. The only choice he had in this situation, was take his ally with him and to escape.
People need to see that Jiraiya is inferior to Itachi in all meanings. There's no way Jiraiya can escape Tsukuyomi and Amaterasu, especially not if someone is using both, able to kill you both with one eye contact and one glance, on top being able to use Susanoo with the Totsuka sword and Yata mirror.