This is how I think it happened:
The original footage was a Killzone 2 E3-style bullshit target render. They quickly scaled back the game but kept the improved lighting, going so far as to work the lighting right into the gameplay. This would be the sequel's big hook, and From talked up the torch system in lots of interviews.
From's assurances that they'd be able to optimize the 360/PS3 framerate in spite of the improved lighting fell through very late in the project. Once it became clear that the older consoles couldn't handle it, Namco had to make a choice:
1. Surgically remove the torch system from the game and redesign the affected areas accordingly
(expensive, delay required, looks good)
2. Rip out the lighting and add a bunch of ambient light to compensate
(costs almost nothing, no delay, looks like shit)
They clearly chose the second option but continued to promote the game with the lighting enabled, right up through the end of January.
Now even though PC hardware can obviously handle the improved lighting, I have a feeling that From stripped it from the PC port as well, just to keep parity with the console versions. After all, releasing a vastly superior version of the game not even two months later would not fly with fans that just spent $60 on it. And it's not like the PC people can complain when the resolution and framerate of their version is still better than the console release!
The improved lighting can easily be added back into the game when the inevitable PS4/XBone port is released, and it will be a great selling point.