So you argument is that Kirin is an actual lightning bolt, and that Rasen Shuriken couldn't compare to nature. But lets look at the facts:
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Here, Kakashi's own "Lightning Cutter", got it's name because he used it to cut a lightning bolt (Which is what Kirin is, in your own words.) This shows two things:
1. Kakashi shows that humans have the ability to react the the speed of it.
2. An S-rank Lightning technique has the ability to cut a lightning bolt.
Now let's move to Kirin:
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Kirin is slow to make, and very situational. But, it is very fast. We all know this.
Now let's look at Rasen Shuriken:
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Super powerful, and cuts on a mircoscopic level. The only known living person to take a hit was Kakuzu, who had his chakra network completely destroyed, and was totally immobilized by it.
Now we have seen that S-rank lightning can cut a lightning bolt, and that it is humanly possible to react to it.
But we're talking about S-rank Wind (And one of the most advanced techniques ever) vs. S-rank Lightning. In the narutoverse, Wind > Lightning.
That brings the only question in to mind:
Can Naruto react fast enough to do RS? We have seen that Kakashi is fast enough, and that Itachi can fully form Susano'o, in the time it takes to strike. And as far as speed goes, Naruto is currently the fastest ninja alive. So he can make it in time to hit Kirin with a RS. Which leaves it simply to S-Rank Wind vs. S-Rank Lightning.
So in the end, Rasen Shuriken will win.