What Akainu did to Iva wasn't even an attack. And yeah, Jinbe was running away because he knew he stood no chance against Akainu. Jinbe blocked one small magma fist from mid range ( = no momentum) using a bucket of water to cool it down, yet having his palm fried. Next time Akainu caught up to Jinbe, he blew a whole through his shark skin, with Jinbe needing medical treatment to survive.
Should I remind you how the entire BB crew ran away from Akainu? When we had Gura Teach who was at least low top tier (overwhelmingly defeating Marco a while later) + Shiryu (at least as strong as Magellan) + the strongest lv 6 prisoners + his original crew.
So you think 3 sweet commanders > Gura Teach + Shiryu + strongest level 6 prisoners + original crew? When the difference in strength between BB crew and Akainu was so big that the BB crew didn't even try to fight him but knew running away is the only wise decision.