Yes, forthcoming DLC packs, "The Battle of Forli" and "Bonfire of the Vanities," were originally intended to be included in the main Assassin's Creed II story. But, as the game's creative director Patrice Désilets told Kotaku, "I felt that, 'Okay, there were too many things to do and to finish.' So we said, 'Ok, let's take a portion of the game that was planned and we'll give it in DLC.'"
The candid Désilets went on to point out, "I think we gave them so much content that they cannot say that we owe them, that we didn't give them a lot for their 60 bucks." So, don't think of the missing chapters as something torn from your disc of Assassin's Creed II that you paid good money for. Think of it as dead content that's getting a rebirth thanks to the wonders of DLC.