I think Akainu has something against the D clan.
He fixates on Ace and Luffy who are both Ds and both Conquerors. There's another part where he calls their blood "cursed".
My personal theory is that Akainu, Dragon and Kizaru were a trio as Marines, but Dragon found out something about the WG that caused him to bolt, and the Goro's manipulated Akainu and Kizaru into thinking that D clanners are evil or something.
There's the possibility of Kizaru being part of the betrayal as opposed to a victim of it, based on Kunie Tanaka's role in Battles without Honour.
Problem is this theory has holes like Saul and Garp being Ds who worked for the WG, so I'll not swear by it completely.