It doesn't matter if Oda intented to give Luffy this power from the start or just recently, the story +20 years old and a lot of things would be changed for the best or worst.
What we need to ask is if this new power can be contected and linked to the story without having a plot hole or not. and what I think that yes we can.
Some people ask why this power just appeared now? Why WG let Luffy free all this time?
For the WG, this power is just a rumor even for the Five Elders. However, the 5Es they know that WG gave this fruit a new name, which might means that WG and the 5Es decided to declare the true power as a rumor and not real due their failure to capture the fruit for more than 800 years.
Probably, after Shanks stole this fruit they decided to not search for it again. And when Luffy appeared 10 years later they monitored it and saw that Luffy didn't awaken it or notice that it have Zoan properites so they confirmed it as rumor only.
Even if they decided to kill Luffy to prevent the worst possible scenario, they would never manage to do that. As they had tried to kill him for different reasons but failed every time. Adding new reason will not change the results.
Plus, WG they don't to kill any one whenever they want like they have the death note, they need to search, investigate, wait for the proper chance then they strike, otherwise they don't need to add bounties on pirates heads.
Its true that WG is a huge power and they can erase entire island from the map like what they did to Ohara, but Ohara is an island with fixed location can be reached anytime, they managed to erase Ohara but they didn't manage to catch Robin, same goes for Luffy or any other pirate they cannot just kill him whenever they decided to.
But the most important question, why they decided only now to kill Luffy to avoid the worst possible scenario?
Simply, Zunisha appearance, the ex-commarde of Joyboy 800 years ago suddenly appeared next to Wano. plus Luffy managed to stand toe-to-toe against the strongest creature on the world as Luffy did the impossbile on this battle.