We cant be sure what the exact reasons were for the lyrics being changed before the song was officially released. Maybe Jive didn't fancy Magic getting litigious over the coke head allegations or perhaps KRS just got cold feet and switched it up himself.
It begs the question of how many other tracks of this nature there sitting in the vaults? I've already covered Lil Kim's withdrawn 2Pac dis, and I recently saw an interview with Clark Kent speaking about a savage dis track Jay Z made (also about 2Pac). There's also the Swizz Beatz produced version of 'Ether' that Large Professor mentioned, and the numerous rumoured shelved/deleted shots between Kane and Rakim. All we have now is Drake vs Meek Mill.