Hyrule was peaceful during her reign. With a natural border of deserts and mountains, it was simply too costly for any neighboring kingdoms to attack, if they had been so inclined. She knew the theories and had read countless texts of war, but the realities shook her, fazed her at a time when she could not afford to be.
To see her men crushed—literally—and defeated was a blow that she could not hide. With a quick gasp, she tightened her grip on her sword, the smallest reassurance she could give herself, and wished desperately for her bow. It was a hobby begrudgingly allowed to her by her advisers, but they insisted that she lead her men with a sword.
Young as she was, she had put too much stock in her advisers' words: more than she ought. After this, she would take matters into her own hands.
If there was an after.
"It is time for you to choose: surrender or die."
Untrained, unprepared for war, her men already defeated, she did the only thing she could do.
The clang of her sword echoed throughout the hall as it hit the ground, and as the dark beasts knocked her men aside in their haste to reach her, she briefly mused that she would have never dropped her bow.
She stands at the window, sees the dismal skies, sees the misshapen kargaroks in the air. It is cold now, when just days ago it was the height of summer. She has taken to wearing a dark, heavy cloak constantly. It wears on her more than she could have realized, the lack of true sunlight. She misses the sun, misses the moon and the stars.
She could leave, she knows. In idleness, she had tried the door, expecting nothing; but to her surprise, it opened smoothly, without even a creak from the hinges.
It was left open, she knew, because there was no where for her to go, no one to help her. As twilight fell over the land, she had seen her people disappear. They were not truly gone, she knew, but now, they are nothing more than barely perceptible spirits.
Surrender or die. Life or death.
She remembered her lessons of the Imprisoning War. Where monsters and beasts appear, surrender does not exist.
Hyrule had fallen before, had risen anew, as the texts told. Hyrule would fall again, she knew, and would rise from the ashes once more.
When Zant put his ultimatum forward, she knew 'surrender' would not equate to 'life.' Surrender would become a rebirth.
Hyrule would die, and nothing she could do would stop it.
And so, she must choose death.
My theory behind this is that as of Twilight Princess, Zelda is so young. She has never seen war, never sent her men to die for her, never seen the aftermaths of battle—much less the fight itself. Add to that a woman who has been taught (most likely extensively) about the Imprisoning War, and who received Wisdom on her own merit: this is not someone who's going to be optimistic about her chances.
And then, add to all of that the fact that Zelda doesn't know that Link or Ganondorf are around: the Triforce doesn't tell her that. She can't possibly know that Link is going to come and save the day. I don't know if the twilight covered Hyrule in stages, the same way you break the twilight in stages, or if it was all at once, but surrendering to a magical madman is remarkably similar to condemning your people to death.
But there was nothing she could have done.