When you first put up "tensions" and "intrigue", I had it in mind that perhaps this was an idea for a game in which the characters muddling is integral to potential disaster. But in a "default timeline that runs out 2-3 years", the players don't own the event. You've scripted something (and put great effort into it), thrust a role in that story upon the characters, and - should the players dare to refuse that role - will resort to punishing their characters.
I keep seeing this notion that consequences are punishment, and I think that is a large part of the disconnect here. In fact, I think
consequences happen based on pc action or inaction is a characteristic of old skool gaming (at least, the old skool I play by).
The whole "don't kill pcs/destroy equipment/use their background against them/enforce social consequences when they attack people in town" approach is a very different approach. In my version of old skool gaming, the players know that they don't always win and may have seen tpks to prove the point. They certainly know better than to expect plot immunity.
One thing about 'world ending' menaces: most of them really don't, even if they win. What happens if the evil empire sweeps across civilization? Well, the world may turn ugly, but it doesn't end. What happens when the archdevil Belial is released on earth? Well, the world may turn ugly, but it doesn't end. What happens if the giant comet hits the world? Well, the world may turn ugly, but it doesn't end. Sure, any of these could result in the destruction of the pcs and everyone they know.
So what? The next party tries to beat the darkness back, Midnight style!
Here's another thing about these things: In a sandbox, the pcs may well not be the only people responding to the situation. Just because the pcs flee the evil empire's advance doesn't mean that the dwarf heroes of Grimhold do, too- and maybe they can hold the evil back.
The pcs
aren't the center of the world in a sandbox. They aren't assured of success. They may not even be the guys that handle the problem.
This continuing assertion that "consequences" are "punishment" misses the point of consequences entirely. They aren't arbitrary, they are the logical result of what has gone before, possibly including the pcs' actions, possibly including their inaction. But I'll put this forward again- if the pcs insist on attacking and robbing store owners in town, is it "punishment" when the other store owners stop opening the doors for them?
I mean, they can't sell loot, buy new weapons (with which to rob more stores!), cash in those gems- is this punishment, or a consequence? If you call it punishment, how do you handle the problem in game, without metagaming it, without saying "Hey, stop that, you guys" to the players? Or do you just blow it off and assume the merchants are too stupid to protect themselves? (After all, wouldn't hiring competent guards be "punishment" too?)