Jiraiya < Pain
Naruto > Pain
Naruto > Jiraiya
IF Naruto > Jiraiya THEN Jiraiya wouldn't have much more impact on the war since there are more powerful people out there.
∴ No, he most likely wouldn't kill or stop Obito.
I like the idea of fusion, if anything it would happen by Sasuke somehow giving Naruto his DNA which would lead him into obtaining the power. This could only happen though if Sasuke will realise what is right and his hatred is ended.