The WG is a joke, if they knew about the fruit they should have send all theirs forces to kill Luffy after he beat Crocodile.
The guy is a D., son of Dragon, Grandson of Garp, have the Strawhat, have this speacial fruit, have been attacking the WG and winning, invaded the three WG main facilities, attacked a celestial dragon, have a Ohara survivor and so many other shit.
Yet the WG is more worried about capturing fucking Shichibukai?
From all the things related to choosen one, Luffy fruir being the choosen fruit was the one i was most afraid that would fuck the story.