Akatsuki wins this fight. The current manga version of the dragon slayers would have been a more suitable challenge, but I think Akatsuki should win even this fight. The battle royale dragon slayers will lose.
Akatsuki is much stronger, can withstand more damage, and has better and more deadly attacks.
Fairy Tail has only one trump card, which is Laxus. He can nullify the effect of Deidara's clay and paralyze Deidara. His Lightning might be effective against Kisame, and Kakuzu was hurt (and in the end) killed by Lightning attacks. But still, this advantage should not be enough to beat the Akatsuki. And furthermore, if there is no prep, Laxus might not even figure out his advantage.
In general, characters from Naruto can be faster than characters from Fairy Tail, but Natsu and Gazille have shown a few speed attacks that would give them an advantage against Kakuzu, Deidara and Kisame (which haven't shown any speedy attacks that couldn't be matched by Natsu or Gazille). But since speed is equalized, this is another point that weakens the dragon slayer's too much.
So, Akatsuki win's this fight, I think even 2 against 3 would be sufficient, e.g. Kisame and Kakuzu vs Fairy Tail. If this fight would be with the current manga dragon slayers, 2 vs 3 might still be enough, but 3 against 3 is still a clear victory for Akatsuki.