Uchiha Yi would not go out of his way to target Jiraiya, but Jiraiya could no longer expect to gain anything from Konoha.
Later, Jiraiya volunteered to leave the village on an intelligence-gathering mission. Uchiha Yi did not refuse, nor did he insist that Jiraiya stay and follow them.
Jiraiya was powerful and capable, but that was all. They would not abandon their plans because Jiraiya disapproved. If he would not accept Uchiha Yi, he was free to leave, so long as he did not betray Konoha.
Jiraiya was a complicated, contradictory man. People called him a hero: he had given his life to bring Naruto Uzumaki intelligence on Nagato, laying the groundwork for Naruto's eventual victory.
In battle, intelligence mattered.
In raw strength, Naruto Uzumaki, who had only mastered Sage Mode, was no match for Nagato. But Nagato had exhausted himself using Super Shinra Tensei, and Naruto had the advantage of knowing his abilities. That was how he won.
Jiraiya had certainly contributed a great deal in his fight against Nagato.
But in the end, Jiraiya was only an ordinary ninja. He was not suited to leadership and lacked a sense of the bigger picture.
During their fight, Nagato had felt compassion for Jiraiya more than once and wanted to let him go. Had Jiraiya left, he could have returned to Konoha, recovered from his wounds, and perhaps joined Naruto Uzumaki, Tsunade, and the others in facing Nagato.
At the very least, Jiraiya could have played a major role instead of dying so miserably in the Land of Rain.
Granted, Jiraiya's death was also a crucial reason Nagato felt compassion after Naruto Uzumaki defeated him and used Rinne Rebirth to help Naruto. Otherwise, even if Naruto had talked Nagato around, he might not have persuaded him to give up