Fred's Hens :
As a person who was an employee, you simply were not in a position of ultimate decision making. You put yourself in a vulnerable position by calling them out, saying you would quit if they did not follow your advice. They called your bluff. You've lost your job.
You are an empath, that is easy to detect. You have strong feelings and compassion and are emotionally involved in the processes at this facility that effects the well being of the animals. Those traits ran head long into the philosophies of the management/owners. To smaller or lesser degrees, all employees face these crisis moments. If you could not in good conscience work to make the place better, or have your voice heard in the decision making processes that allowed you to live with the outcomes, then it is best you for you to have left.
Perhaps one day you will either work for a place more in line with your own ethics on these matters or perhaps even own your own facility or be higher in the management, decision making administration of such a place. Then, your voice would be heard. Until then? It's best you try to move on and get on with your life.
x2.
Do not feel badly because the decison was not yours.
I am sure your next job will be where someone appreciates how wonderful you are with animals, therefore, everything will be better for you as well as the animals under your care.