As you say, there is unfortunately precious little I can do to prevent things like this from occuring. And when faced with the choice between 1) leave things as-is because I might break someone's savegame, or 2) make things better, do things more efficiently, and fix bugs, #2 will always win.
I have done some steps to prevent this from occuring with GlobalVariables when an update is received. I had an "Oh, sh$!" moment a few days ago, when I almost pushed a simple update without testing it, but at the last second decided, "Better take a look anyway". Loaded a game saved with a previous version of my mod, and to my horror, my character keeled over and died instantly. Boy, that would have been a PR nightmare.
What went wrong? I was performing the check, "if Exposure Points == 0, kill the player." Guess what? Orphaned GlobalVariables in a savegame, when not used, seem to initialize to zero or 0.0. I had an orphaned GlobalVar that was instantly killing the player! This was on top of my EP still reporting 100/100. I prevented it by saying instead, "If Exposure Points < 0, kill the player." The truth is that, based on the math, Exposure Points would almost never equal exactly zero, so it worked out. It seems like if the game is performing that kind of a condition check, "If 0, if 1, if whatever", it will look for every matching GlobalVariable, and if -any of them- match the condition, it will return true. This is unbelievably stupid, because they made this an implicit OR.
In other global variables, I have started using 1 and 2 instead of 0 and 1, to ensure that globals initializing to null/FALSE/zero won't have an affect on my logic.
But yes, this is a script-centric mod, and it's not done. I will note, in bold font on the OP, to back up your savegames. I'm hoping however that v1.4 will "un-stick" many people's games, as it relates to being able to Fast Travel, which is not controlled by an errant script or global, but purely a function call to Game.EnableFastTravel(True).
Also, Thomas, if you don't mind, could you try something for me if v1.4 doesn't fix your issue? Can you open the console, and type, "set _DE_ExposurePoints to 75", get near a fire, and see if you start warming up? If you do, then things should be working normally for you. Let me know.