Well, it shouldn't help. Killing or sealing black zetsu would be very difficult unless fujin has sage of six path's level sealing. Naruto and Sasuke had to seal away black zetsu in the end along with Kaguya because they couldn't kill him. There would be too many other obstacles too. He doesn't have nine tails chakra, so he wouldn't be able to distinguish between ninjas and white zetsu. Black zetsu is probably even more cautious than orochimaru. Do you honestly think that black Zetsu and Madara wouldn't have any contingency plans? After all, going unnoticed by the whole world and manipulating it for thousand years isn't a simple task. Forget about these, let's not forget that there's Toneri out there on the moon and Isshiki hiding somewhere in the world. Then there are whole bunch otsusukis that will be coming later. Unless Fujin is six path's level around final battle timeline, he would sooner or later just get killed because Naruto is full of powerful threats.

To Author- The way are going currently, Fujin will reach maximum high kage (around or a bit higher than pain's level) with sage mode. But unless something is done over time, getting to super kage (Hashirama and Madara's level) and six path's level (Jubidara level) would be impossible for him in short amount of time. Since Naruto is mostly about purity of otsusuki bloodlines, if you're planning to have any other route than becoming ten tails jinchuriki (which might not be possible for him because even obito wasn't able to control it that well with Rinnegan, plus it doesn't look safe because it's the part of Kaguya's chakra in the end), then you'll need to plan something good over the remaining 3-5 years before shippuden events.

To Author - I hope you have some ideas ready about making Fujin six path's level in next few years. Naruto and Sasuke could easily become six path's level in the final war because of Asura and Indra's chakra. But fujin won't be able to do that. So, you'll need to gradually increase his power to six path's level before events of shippuden start. Also, you might not need to worry about Fujin becoming overpowered because Fujin is already quite cautious in nature. So, there would be many reasons for him to keep most of his power hidden till last battle.