Hiruzen Sarutobi had plenty of problems, but he was not a bad person at heart.
For now, Hiruzen could still keep the situation under control. After the Fourth Hokage died, though, he chose to become Hokage again to keep Shimura Danzō from taking the position. By then, he was no longer the man he had been during his first term. His grip on Konoha was nowhere near as strong.
Uchiha Yi could roughly guess what had happened. Unable to control the situation, Hiruzen had let tensions within the Uchiha Clan grow. He could no longer keep Shimura Danzō in check, either, and Danzō began doing as he pleased. Even when Danzō tried to assassinate him, Hiruzen let it slide.
In Hiruzen's eyes, Konoha had been far too weak at the time to withstand any further turmoil. He could not afford to move against Shimura Danzō.
Of course, Jiraiya and Tsunade shared some of the blame. Tsunade was understandable, at least. She had no interest in becoming Hokage, and by then, her heart was already dead.
As for Jiraiya, whenever anyone needed him, he was nowhere to be found.
Just like now. The Second Shinobi World War was still raging, yet Jiraiya had run off. If he had not been Hiruzen's student, with Hiruzen covering for him, he would have been branded a traitor and a deserter.
Jiraiya would not be in Konoha during the Nine-Tails' Attack, either. He would probably be off wandering somewhere.
When Hiruzen needed Jiraiya most to become Hokage, Jiraiya would not stand with him. Becoming Hokage would not have been difficult for Jiraiya, and he would not have been a puppet. He would have been far better than Hiruzen in his second term.
When Naruto needed Jiraiya to look after him, Jiraiya would not be in