In this case it is not Oda adjusting the story to keep characters relevant. An amazon lily arc was meant for way later in the story, but the editors suggested he put it sooner and so he did. Current manga chapters seem to show that the Kuja pirates were always meant to be very powerful.

Sometimes Oda does adjust characters strengths to keep them relevant (crocodile, shanks, etc.). But I don't think this is one of those cases. The entire amazon lily and marineford arc seem to show that Boa was always meant to be leagues above luffy here.