Interesting that a state level Department of Game and Inland Fisheries has the authority to supersede federal laws, especially where the process has occurred repeatedly to protect what is very likely a backyard flock. What state and officials involved?
THIS IS NOT LEGAL ADVICE AND I AM NOT A LAWYER.
These are just my observations and understandings from numerous phone calls and emails to government officials today. I just spend a good portion of today nailing down the details on this very topic. In our state (Maryland) it is not considered a crime by the state authorities to defend your livestock or crops from a nuisance predator. The state DNR police told me that they do not even investigate or prosecute these cases at all. They actually didn't even know how to advise me and referred me to Fish and Wildlife instead. This is even stated very clearly in the State regulations.
http://www.lawserver.com/law/state/maryland/md-laws/maryland_laws_natural_resources-10-401
(b) Unless prohibited by federal law, this section does not prohibit a landowner or his agent from shooting hawks or owls when considered necessary to protect poultry or game birds or mammals on the landowner’s property from destruction. In addition, this section does not prohibit the Department from controlling birds or mammals which have become obnoxious in nature or habit or are damaging wildlife on any lands in the State.
HOWEVER, it is still a federal crime to harm, hunt, pursue, injure, possess, etc, any migratory bird (this includes all birds of prey) without a permit. There is a permit available for killing a nuisance predatory bird called a 50 CFR. There are many restrictions and a significant cost involved. Additionally, my impression was that no hobby farm or suburban flock could hope to meet the standard required to have one issued. (This was simply my impression from the conversation, it was not actually stated explicitly) There is also a provision in the federal statute that allows for the "scaring" of these birds without any permitting or permission. I was actually calling to get some guidance on that particular issue. They told me that anything that does not physically harm the bird is permissible. Electric fencing, electric perches, fireworks, noise makers, motion sensing sprinklers, protective animals, netting, wire perching deterrents, were all discussed without any concerns from the official.
Please do your own research as I am just an idiot mechanic and the federal penalties are substantial for this infraction. They include significant prison time (of course in federal prison, not your local jail) and 10s of thousands in fines plus forfeiture of any materials used in the commission (your car, your gun, your house). This is just my own experience in my own state.
Andy