A couple of options spring to mind:
1) Get a noise fingerprint from the rotors and clean the audio with DSP. Hard because the noise of the rotors is constantly changing, but you could potentially place several contact mics next to the rotors and then subtract that from the main mic to get a cleaner signal
2) super directional audio with parabolic reflectors which reject audio outside the narrow beam
3) Don't record audio from the drone! Use wireless mics on the ground instead
Disclaimer: Used to be an audio engineer in past life and have been running a drone company for 3 years. We specialise in high end video (RED Epic), but are also working on some non-cinematography applications at the moment. We have both hardware and software teams. Any investors interested in hearing more, you can get in touch at info@londonhelicam.co.uk