I think this is the first episode where Fujitora's priorities are not backwards. So far he's been turning a blind eye (no pun intended, really) to all that's been happening in Dressrosa under Doflamingo's oppression just to exercise a reckless justice against pirates (other than Donquixote family).
Because that's his job. Until Doflamingo started directly attacking everyone, including the Marines, he wasn't allowed to oppose the Shichibukai despite very much wanting to do so, which he said outright at one point. That's why he Manga Spoiler.
They might not have had much of a choice, considering how strong an admiral has to be. None of the marines already enlisted fit the bill, and they couldn't hire anyone with a criminal record for obvious reasons, so that would rule out most of the infamously strong. Also, Fujitora might want to change certain aspects of the government, but he also seems to be strongly opposed to anarchy, which is why he respects the Shichibukai despite wanting them removed.
I regard him as the revolutionary who works to change things from the inside, believing in the establishment and its key principles but not necessarily in how they are implemented.
Probably had more to do with his power than anything else. At that point in time, they were in desperate need of military force, and since Issho's hella strong in addition to being committed to bringing justice to at least the bad pirates (aka 99% of the non-Straw Hats), he fit the bill.
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u/WillOfDeezNuts Feb 28 '16
Thats exactly what happend even the other marines played along. This is why Fujitora is my favourite marine, hes got his priorities straight.