In short terms: No.
There are people on here that are saying that Naruto could "sense" Kirin, and move accordingly, but you have to be realistic about Naruto's fighting style. While Naruto is somewhat like Albert Einstein (the guy was a genius, yet couldn't tie his shoes, while Naruto is stupid with books but a tactical genius) to elude this technique, he'd have to understand it first. To sense and just think, "Maybe I should run", isn't like Naruto at all. Naruto in Sage Mode is not as fast as Raikage, so there isn't anything telling me that Sasuke's Sharingan can't keep track of him.
However, does he have the means to counter it? It's possible. If he prepared a Rasenshuriken and launched it at Kirin, it may overpower the move since Wind>Lightning. I'm not too sure about natural lightning, but considering both are S-Ranked techniques it's possible that he could simply throw a Rasenshuriken at Kirin upon sensing the danger.
If it hit's Naruto, he's a goner. However, Zetsu implied that at the point that Sasuke awakened the Mangekyo (AFTER using Kirin) and Naruto's fight with Pain that Naruto could take Sasuke. IF and only IF we hold this as true (Zetsu isn't too trustworthy, but I don't see any indicators as to him lying other than conjectures by hardcore Sasuke fans) it is possible that Naruto would survive a fight with Sasuke. Do not forget that Zetsu explained the technique to us readers, AND saw the fight against Pain.
Also, Frog Kumite might make him able to sense danger, but the problem is Kirin has such a large explosion range...