The original members of the Philosophers died in the early 20th century, as the Boss tells Snake in MGS3. It's those names that Otacon found in the disc.
The "revival" that Ocelot speaks of has nothing to do with computer AI. Boss also speaks of how the Philosophers had become a shadow of it's former self. They no longer had any power. But with the help of the legacy, the US branch could finally be revived.
As for Rose and the Colonel in MGS2... Rose is real. Up to the point in Arsenal where she is about the tell Raiden that she is pregnant. After that, she is switched to an AI. The Colonel, however, was always an AI in the game. It's pretty obvious really, if you think of his way to speak. Always talking about how it wasn't a part of the simulation and bla bla bla. "Complete the mission" yada yada. The Campbell I know wasn't like that in MGS1.