Speaking to US mag Game Informer, Hideo Kojima revealed new gameplay details on Metal Gear Solid 4. I haven’t been able to read the interview myself yet, but here are a few quotes taken from a CVG article.
Caught in the middle of a near-future war, Snake must blend in with the two warring factions to remain hidden, whilst avoiding starting conflicts with both sides.
"If, for example, Snake's mission's goal was in the battlefield of A vs. B, Snake has the option to interfere in the battle or not," said Kojima. "To complete a mission, the simplest way will be to sneak into the battlefield without getting noticed by either A or B. However, if he is attacked by Country A, and kills a Country A trooper, that means he becomes an enemy of Country A. So if he continues to fight Country A, that makes him an ally of Country B, and that makes him a hero from a Country B side point of view."
Source: Game Informer via CVG