In any case, they most certainly cannot 'generally' avoid rotors. I have seen birds of prey - as well as smaller birds - attack and/or collide with UAVs. I have never seen a bird escape uninjured except with a small quadcopter with plastic blades. If someone was orchestrating a terrorist attack they would obviously need some sort of payload, and would not be flying a palm-sized plastic-blade quadcopter.
I think eagles are cool and they're clearly majestic creatures. But using them to catch a set of spinning blades in the sky - when a bullet works just fine - is really stupid.
Anyway, birds learn so you can train them to avoid the blades. Shooting something near buildings is risky and loud even with buckshot. Birds can also follow terrain etc. So, while this is far from perfect it's not a terrible or useless idea.
https://en.wikipedia.org/wiki/List_of_birds_by_flight_speed
As to rotors they can generally avoid them. However, this is just for off the shelf drones, you can build something that can get past them but it's a lot more effort.