This is an awesome idea of course. It's a glimpse into the future. I remember tweeting with Chris Anderson of 3D Robotics about a year ago about autonomous package delivery from A > B. I'm sure Bezos and team started nerding out on this concept years ago. Eventually, "vehicles" the size of UPS trucks will be delivering packages autonomously all over the world. This is definitely a glimpse into that day. And it won't…
I can imagine FAA approval subject to a register of drone flightpaths and locations, but if something takes a knock from a bird (or malicious interception, as you suggested), I assume that Amazon would schedule a manual pick-up and replacement, wearing the cost in the process.