The mass slaughter (pain) was Nagato's answer to the question of peace. Jiraiya and Naruto's was the opposite to that. Naruto's words (and his own that he had forgotten already) convinced Nagato that he had erred and he decided to switch back to the path he once believe in. In that sense undoing the deaths was quite natural. Under most circumstances I'd have thought it a poor choice by the author but not in this case since Nagato's return made all the death invalid. It could be said that they would have served as a measure of Naruto's real conviction of not leaving Jiraiya's path no matter what, but requiring such a thing would have meant Nagato hadn't really believed him. If you demand proof for something, it indicates lack of belief, after all.

Well, I can't really explain why I don't mind this particular case of resurrections any better than this. Typically I view every good story needs good guys dying - due to having Les Miserables as one of the very first novels I ever read - so I deem I hold some perspective.