He doesn't even need to get buddy with pirates, if he has the authority to arrest Doflamingo then he can attack Doflamingo and end this.Since when is an admiral of the navy an patsy of some pirates ?
I agree that Fujitora should not be working alongside the pirates, and so far everybody inside the cage is safe. Also Fujitora already threatened Doflamingo. So if there is anything he should do is see this fight end and take Doflamingo with him to topple the shichibukai system.
Doffy already said that there is no coming back from this, he already lost even if he wins the fight with Luffy.
Fujitora in full health can step in and take out Doflamingo whenever he wishes to. But his hands are tied as a marine at this point .
If his hands are tied from fighting Doflamingo then he can't arrest him, as that would still be considered attacking him.
In fact the World Government would probably prefer it that he stopped Doflamingo when you consider what happened with Crocodile.
And considering they are minutes away from the death of people who aren't pirates, he can help slow the bird cage without any rule violations.
They are only 3 minutes before people who aren't pirates start dying so they are all in danger.
Edit: Also, the World Government and the Marines get patsy with pirates all the time, that was the very idea that led to the Warlord system in the first place.
Use pirates to fight pirates, the World Government would have no problem if he got the aid of pirates as long as they can cover it up and make it look like he did it alone.
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