As pull-up and pull down resistor and the wiringPiISR library call did not work for Banana M2-Zero I modified the BPI version and (partly) fixed the problems. More details in the README file on my github. As stated in the README I did not test every command, just the ones I needed myself.
If you need a command or library call which is still buggy ( for M2-Zero) let me know and I will see what I can do … wish you fun
example of (corrected) gpio readall:
Im getting this error when building:
GPIO Utility
[Compile] gpio.c
[Compile] pins.c
[Compile] readall.c
[Link]
gpio.o: In function `doEdge':
gpio.c:(.text+0x7d4): undefined reference to `bpi_translate_towPi'
collect2: error: ld returned 1 exit status
Makefile:55: recipe for target 'gpio' failed
make: *** [gpio] Error 1
Im trying to investigate why this happen, and how to solve it. Which inage do you use to buid it?
[SOLVED] I needed to uninstall the original WiringPi of the image
Worked like a charm. Thank you very much!!! 
I measured up to 8 khz which is the same as Rpi.
I tested it in the 3 pins of the example isr2, on a BPI-P2 Zero that is very similar to a M2 Zero.
This is the example I used to test it, if you want to add to the examples folder isr3.c (2.9 KB)