Yes, randos not working for the WG. Why would Akainu be against his own military having weapons to nuke evil?
WG is NOT Akainu's military...
WG is the ruling govt of the world. Marines are their army, but it's also it's own organization.
WG having Ancient weapons is not the same as marines having it. Far from it actually.
Akainu is not satisfied in his current position where he's under the thumbs of the CD and the gorosei. He literally calls out gorosei to their faces and straight up asks if they're being controlled by someone higher up.
Recent chapters literally spell out Akainu's dissatisfaction and hint at him possibly rebelling against the WG. We had his encounter with Kuma where he questions Kuma's status as a puppet on strings, while in the background, random CDs berated and insulted Akainu.
Oda could not have been any less subtle about Akainu feeling the same way about his situation and comparing himself to Kuma.
So yeah, Akainu has reasons to go against his masters.
He's all about ABSOLUTE JUSTICE.
If he feels the WG are not on the side of justice, he wouldn't hesitate to bite the hands that feed him.