Fujitora's character is in an interesting place this arc, at his heart he is a good man who wants to make the world for the better, abolishing the corrupt pirate Schibiukai system and such. But in this place (Dressrosa) ruled over by an associate of the navy, by his title he can't do anything to stop the corruptness going on there, thus he has no choice but to leave his "bets" on the pirates to take down the corrupt leaders of the country so he might be able to change things after.
He does have his justice in the right place, he's just conflicted with what he can and can't do and what would be better for him to do in the long run.