@Black Angel Firstly, I'll admit that I have not played the game.. As for the colony, I feel that the colony may detract from the grim situation set up in the short story though from a design perspective, the addition of the colony probably was implemented for a happy ending for players who achieved the good ending through trial and error since the short story ended on a downer for everyone.
One thing, though, from what I've heard the author of the short story actually voice-acted AM in the game. In that case, we should've contacted him if he's okay with the changes made by the game.