It's more than a little weird, it's annoying for me and the reason why I say Fujitora was at the very least held back in terms of his display of strength (though I guess that's the case for a few characters in that arc).
I think the difference between Doflamingo and Crocodile in that aspect is that DD was already a king as well as being a Shichibukai; so he wasn't trying to destroy Dressrosa, rather keeping everyone within the Bird Cage so he could eliminate them before they could escape or outside support could come. On top of that he also had insights and knew things about the Celestial Dragons that gave him bargaining power and was able to use that to dispatch CP0 to him and also manipulate the press for his own benefits.
Was Crocodile trying to take over Alabasta or just using it as a base of operations and means to recover the Poneglyph? it's been such a long time.
The WG turn a blind eye to a lot that the Shichibukai do as long as their actions don't jeopardise the agreement they have and they still fulfill their other duties. Look at Moria for example; if Kuma knew to find him and offer him help( I THINK the WG actually sent him there IIRC), certainly the WG had an idea of what he was doing.
Crocodile used the rainpowder plotdevice to make the citizens think that King Cobra was stealing the rain from them, causing the revolutionary war while Crocodile appeared as a hero in their eyes. He also tried to kill both king Cobra and the revolutionary leader Kohza and tried to blow up both the royar army and the revolutionaries with the bomb that failed to even kill Pell.
The marines didn't know about his doings until Smoker found out he was the leader of Baroque Works in the casino. He went so over the top with his Shichibukai freedom that there's no way he wouldn't get his status revoked and arrested. There was also the thing about Crocodile actively trying to find one of the ancient weapons to wage war on the world but I don't know if the marines even knew that bit.
I guess the difference with Doflamingo is the Celestial Dragon stuff, and that thanks to Sugar's power I guess that nobody remembers that he's not even the rightful Dressrosa king.
I think Fujitora was following orders to a T, but given that Doflamingo was trying to prevent any knowledge of what was really going on from leaking, and Crocodile was trying to keep his activities secret, I'm sure WG had a limit as to what they could and couldn't do. The WG wouldn't risk the shichibukai damaging their image by doing horrific stuff so they'd try to stop them if they could, but given that the shichibukai did also represent WG, I guess the government also had to consider the pros and cons.
Once Doflamingo activated Birdcage and started slowly but steadily compressing its size, he instantly become a mass murderer. I don't know how many citizens actually died, but he intended to keep the cage up until all the strawhats, Law and the rest were down. If his fight with Luffy had lasted hours, which isn't an unusual duration for this kind of high level fights (like Luffy vs Cracker lasting all night) then the cage would have been reduced to a minimun size and everyone in Dressrosa except Doflamingo, Fujitora included if he still had decided not to attack and stop Doflamingo, would have been compressed and cut up by the strings.
We know that Fujitora couldn't contact the exterior when the birdcage started because the birdcage somehow cut "even the phone signals", but I want to think WG would have allowed to stop him at that point if communication had been possible. So if Fujitora didn't attack Doflamingo then would be because he wanted to stick to his last received orders, however, this is the information Fujitora had at the point the Birdcage started:
-Thousands of citizens could have potentially died if Doflamingo wasn't stopped.
- Fujitora himself was in harms way because of the birdcage.
- Sugar's technique had been undone and everyone suddenly remembered King Riku, a king affiliated to the WG, who was now again human and also in harms way.
- Now everyone could also remember that Doflamingo has stolen the kingdom, which is also a very heavy crime.
In my personal opinion, once it was come to that, Fujitora should have attacked Doflamingo. Since all possible communications were down, he could have later just lied and say that Doflamingo was taken down by a pirate like Luffy and that he had nothing to do with stopping him (making the situation the opposite of what happened in Arabasta).
I don't think the Marines had an issue with making Smoker look like a hero for stopping Crocodile, did they? I wanna know if Smoker or Fujitora would try to stop another shichibukai or if they'd still not do anything.
We will never know, since Shichibukai's are no longer a thing, but I always loved how Smoker handled things in Arabasta. He trusted the strawhats to kick Crocodile's ass and went behind their backs to steal a rainpowder ship from the Baroque to make it rain on the war and stop it. He's the one that actually stopped the war, and then told the admirals to go eat shit when they told him they were making him the hero who stopped Crocodile. Gotta love Smoker as a character.