Akainu is constantly saying how busy and hectic the Marines are. Imagine the US is about to finish the Manhattan project, and the intelligence agencies try to kill Einstein? It's just ridiculous.
Akainu is relying on the Seraphim to replace the Warlords, and CP0 (who we KNOW is outside of Akainu's control based on the tantrum he threw to the Gorosei during Dressrosa) is trying to murder the guy who is making the Seraphims Akainu needs to maintain order. Akainu should be PISSED when he finds out about this.
It's clear Akainu wants to actually destroy pirates, while the WG wants the Yonkou to exist to maintain balance and order, so Akainu and the WG are at odds here.