Because the company can't afford to feed them.
The JTA has some of the story:
…Multiple sources told me that employees were ordered to kill thousands of unused chickens, apparently because the company couldn’t afford to feed them (but if they could afford the labor to kill them, why not slaughter and sell them?).…
The answer to the JTA's question is as follows:
1. The chicks are at large factory farms owned by the Rubashkin family, not at Agriprocessors.
2. These are baby chicks, too young for slaughter.
I spent some time earlier today trying to find someone who would raise these tens of thousands of chicks and then donate them to charity.
Unfortunately, there is no way to make this happen.