It's not about giving him a leave but Akainu still maintains a very friendly tone with Fujitora even after all his fuck ups, unnatural from an angry boss.
Here its isn't like who has more degrees or experience to be the boss and always shows his frustrated/hot side rather than it's just strength which keeping them in two different positions while we all know the difference won't be that huge for Akainu to show his attitude all the times.
Fuji knows how corrupted the WG is already yet is still fighting for the navy, so knowing a bit more about the past should really change his stance. If anything I think Fuji's role will be to maintain the navy's reputation and solidarity during the WG collapse in preparation for his future FA role.