TIM6 would also work, but it shares an interrupt vector with something else. The other non-basic timers would work too, but they have nice features like PWM which would be wasted on this application. I only tested on Crazyflie 2 so far, but TIM7 is available on the STM32F103 too.
I would be happy to contribute this code to the main repo if desired. My changes are visible at https://github.com/jpreiss/crazyflie-firmware.
Really cool project by the way
