The FAA's first round is out, with the proposed "drone pilot licenses" and coordination with existing ATC for drone operations in controlled airspace. That won't scale up to large numbers of drones, but can be done now. The FAA is considering fewer restrictions on very small drones (<2KG). They have a study indicating that in theory most 2KG drones won't damage large aircraft jet engines enough to destroy them. But as yet, that hasn't been tested on real engines. (Real engines are tested against bird strikes by firing frozen chickens of various sizes into the engine, using an air cannon. That's going to have to be done for drones, and it's not cheap.)

The FAA is trying to get this under control before some large quadrotor with motors with cobalt-neodymium magnets gets sucked into a jet intake.

[1] http://utm.arc.nasa.gov/index.shtml