I really doubt that , don't see why they should fight. Koby is part of sword who clearly has an agenda that goes against the WG and so they will most likely allies than enemies, the wrongdoings of the WG are gonna be known for everyone soon. don't see why good people should fight good people.
I can understand why Garp fought Roger or why Smoker always tried to fight Luffy but at the EoS it will be clear good vs evil.
the WG still has some hidden powers , like the power which forced that Kozuki to isolate Wano. Luffy needs the good and just marines to be on his side.
Luffy befriended even People like Bege and Kid and work with them together and we saw him no matter how Smoker wanted to fight Luffy at the end of the day he helped him.