He hates the idea of the WG playing god aka CDs
And his concern towards the WG, the Warlord system, was done away with. He’s shown no other issues with the WG.
In reverie he walked on top of ground with slaves under foot.
In reverie he was friendly with Ryokugyu who refers to the CDs as gods
Post reverie he talked to Sakazuki about how we in the marines need to put faith in Child soldiers
Just like how Kuzan doesn’t fully agree with Bb, Fuji doesn’t need to fully agree with the CDs, but he clearly harbors no intention to betray them.