When something smells of ammonia - its off, past its use by date, not properly processed or stored, to me. When I've kept chicken or fish a bit too long and it smells like that - I bin it. Even though the fish may have cost way too much, or I was looking forward to a chicken curry dinner, once it has that smell, it's out of here.
It's an instinctive thing to me. That smell means don't go near it.
The smell at the factory was most probably the smell of their droppings, to be polite. That's why the overcrowded fowl get hock burn, they have nowhere to get off the floor which is covered in....well...you know. Not a nice life for them.
I can't afford to buy organic/free range birds, but can't say I've noticed the factory fowls smelling of ammonia. If it does - toss it. Have the rice and veg instead