Ah, those irritating news headline 'quotes'...
I don't necessarily want to dispute the result itself, but the way the story has been reported is somewhat misleading. If the average religious believer is less intelligent by some measures than the average atheist, that doesn't necessarily mean that "atheists are more intelligent than religious people". It carries the same sort of meaning as "women are more [insert quality here] than men". There is some natural variation around that, and the statement, while it has some truth, is misleading.
In that sense, then, this is both similar too, and different from, "the old debate", whatever that may be. Similar, because of the (attempted) application of rigour to analysing an idea. Different, because the conclusion is being given to us by a paper and I don't know if I support the way the headline is phrased.
Unfortunately, the actual study appears to be trapped behind a paywall, so I can't make any more specific comments.