Real documentation for this game would be so very appreciated.
I think you'll find that there are very few games around which document the game in that level of detail. The vast majority of games take the line, "Find out in the game", thus encouraging players to test out their theories in the laboratory of the game. It's also a reward mechanism - the moment of insight when one figures out a mechanic is a "warm fuzzy" to most people.
If they did as you suggest and documented everything - this would just be a spreadsheet with a graphical front end.
If you want 100% documentation, I advise you to stick to chess or the like.
As they are, plagues are really just a "stupid game hates me" kind of thing.
I think that's a design decision, to occasionally throw the dice of fate. Most games have it, be it the deviation of bullets from your cross-hairs in a FPS, to a volcanic eruption in Civilization. I think you have to consider the intent of the design decision. It is, or was intended to be, a fairly minor event which would disrupt a player's plans but not cripple them. That it spread so far and wide with such a devastating effect as in Osito's case, was a bug - which Elliot has hopefully exterminated.
That said, I agree with you that there should be something that a player can do - crash research for the plague, quarantine of the planet or the like. But given the time and resources available to Elliot however, it's probably a not on his "red flag" list.
If you really dislike this sort of thing, you can disable disasters on the "victory conditions" panel when starting a new game.
“That which can be asserted without evidence, can be dismissed without evidence.” ― Christopher Hitchens