Spoilers about the game's story follows.

If you're okay with spoilers, read on.

Here's my theory:

Project Zero Dawn was proposed because Dr. Elisabet Sobeck was NOT an expert on military technology

The game has a hologram recording of generals suggesting they could send unmanned bombers to attack the rogue machines, and Elisabet responded that they could not send anything automated because they would end up getting hacked.

Disregarding the issue that the nanomachines responsible for the Plague can take over electronics of a different architecture and programming language, Elisabet seems to have little knowledge of non-electronic weapon systems that could still make a huge impact against the machines, like nuclear artillery platforms.

Let’s take the in-game strategy of giving recruits railguns, who will end up being just cannon fodder anyway. This is horribly inefficient if you compare the effect of a railgun to a weapon like the M-29 Davy Crockett, a man-portable nuclear launcher. In real life, this weapon was never used because it was a suicidal weapon, but in the context of a robot war apocalypse, this kind of weapon would be critical.

Another alternative would be to send birds, dogs or various other animals to deliver the nuclear payload. No human lives would be lost, though training the animals to hit the right targets would be hard.

Dr. Sobeck, however, did not know about weapons like this (which makes sense because she was never involved in weapons development, and her robotics was focused on peaceful use).

The terrible side-effect of this is that Sobeck couldn’t develop a strategy to exterminate the machines, and instead opted for a risky solution. The generals in the room didn’t mention any of this, because they made the false assumption that Dr. Sobeck already considered the use of portable nukes.

While Elisabet’s plan did work out in the end, it seems apparent to me that Project Zero Dawn was only proposed because Elisabet wasn’t an expert on weapons.