Your version...
If ........>Konoha could be completely destroy.
Story to start from Jiraiya returned to Konoha after getting info from Pain.
No chakra rod. No Pain dead body, etc. Also Danzo killed the Toad - not such happening.
Scenario 1: Jiraiya bring Naruto to learn Senjutsu.
Jiraiya told Tsunade that Naruto need further upgrade - Senjutsu.
As we know now, Kurama did not allow to share room with the toads.
Jiraiya would suggested other methods for Naruto to learn Senjutsu. As Master is always right decision!
Jiraiya unable to foreseen Pain to attack immediately, thus this affect the training period, longer days.
Jiraiya continue his story writer, while Naruto was training. No urgent required.
Meanwhile, Pain came and searching for Naruto only.
Anybody being questioned will die. Tsunade die. Konoha destroyed. Danzo and his men will die also.
Knowing Naruto was training, Konoha become totally empty, and hid themselves to wait for Naruto returns.
Naruto with Jiraiya returned. Encountered Pain, the fight began.
Did not had the most important information from Kakashi, - need 5 seconds to change another jutsu.
Naruto cannot use his flying rasengan.
(Note. In actual manga, he sneak out during night, to upgrade his rasengan.)
Hinata was dead, so Kurama chakra was not activated.
Scenario 2: Do Nothing. No Senjutsu.
Jiraiya told Tsunade that he would train Naruto himself.
Pain came and partly destroy Konoha. Naruto was taken away by Pain.
End
