Whenever Natsu ate an "explosion", he only ate the flames erupting from it... the explosion itself clearly affects him.
Akainu still has physical attacks and logia intangibility + Regenerationn. Natsu is not going to kill him with the current knowledge on logia devil fruits. The only way he is going to kill Akainu is by somehow luring him to a body of water and dipping him in it.
Akainu, even if we suggest his magma would have 0 effect on Natsu, still has pre-cognition (if we suggest he keeps CoO instead of CoA) and enhanced visual powers along with his insane physical capabilities. He stopped a two-armed swing from Whitebeard with nothing but his foot and could tank two blows from him and continued fighting every pirate still running around on Marineford including Marco and all other WB commanders + Crocodile.
Even if we take Akainu's logia intangibility and attacks and removed them, Natsu would still have an INCREDIBLY hard time beating him due to Akainu's superior experience, and willingness to kill his opponent on top of pre-cognitive powers OR barriers/enhanced attacks (since we're going to limit him to 1 type of haki).
Natsu has only displayed adept level close quarter abilities, as more experienced fighters like Gildarts could easily evade and counter him due to the openings he would leave. Akainu, being an Admiral, surely has gone through much more intensive training and experience than CP9 members.
Which brings us another thing: Vice Admirals and Admirals also have at least adept capabilities in
ROKUSHIKI.
I stand by my original statement:
Akainu wins Low Difficulty