Of course Konami would be reluctant to end the Metal Gear series; it's one of their biggest franchises. While Kojima has insisted that Solid Snake must meet his end in the upcoming MGS4, it doesn't necessarily mean that the franchise will be over. Ryan Payton told MTV Multiplayer that "I think there's been some misconceptions that this is the last 'Metal Gear ... This is really just the last chapter of the saga of the Solid Snake story."
The franchise has many other directions it can go, but until we play through Snake's latest saga, we won't really know where. Perhaps we'll play as someone completely new, or go back in time once again (a la Metal Gear Solid 3). There are tons of possibilities.