Not to offend anyone, so I won't say much but do you really think Doflamingo is on the same level as Crocodile? Hell, if anything that page I provided you exactly shows that they're not, even the Fleet Admiral of the Marines were CONFUSED on the matter.. Sakazuki went to Mariejois to try and resolve that. Fujitora can't act due to that.. please tell me you can understand that..
The confusion was due to the Warlord resignation/resignation retraction debacle which Doflamingo pulled through CP0. He was still very much under suspicion due to the events at Punk Hazard; Fujitora says that him being Joker would be serious business, and Doffy asks him to provide proof (how on earth they did't have any proof after Punk Hazard is beyond me).
Now, its not a question of suspicion anymore. Fujitoras groups are first hand witnesses to Doflamingo comitting an offense to the law of ASTRONOMICAL proportions. Marines are being used to murder innocents. Theres no wriggle room left for Doffy, no misinformed reports or retractable statements. Saying Doffy should be protected because of that scene is like saying that if a druglord avoided being convicted because of insuficcient/tampered evidence, he'd ALSO be safe to just go shoot off someones head in front of a police officer directly afterwards.