Guess I'm funny that way - I call a multiplayer game one that you actually play against another player, in the same game - but maybe that's just me.
Anyhow, using a fixed random number seed would solve the problem you are describing. If they did this, then everytime you hit the anomaly you would get the same result. As the game stands, you can use multiple reloads to change the colonization result on each load, so this problem exists independently of anomalies.
But any way you cut it, making a game "tamper proof" or even a little bit "tamper resistant" when the data resides on your hard drive, is problematic. Its just way too easy. If that's the way the Metaverse is implemented then there's going to be lots of people out there that find it easy to cheat.
Putting the saved game data on the server (as Diablo does for their competitive rankings), makes it much harder for people to cheat (although even then, people complain loudly about exploits and hackers). If the Metaverse were implemented that way (and for all I know, it is), then you wouldn't care about people tampering with saved game data in standalone games.
Bottom line, us standalone players really want a game that plays continuously, without weird save/reload issues. This is a critical feature for those of us who can't afford to play more than an hour or two at a time (or leave it running permanently, like Iztok Bitenc does).