My is "whining" also on PETG. When I first printed in PETG I thought that the fan is broken.
That's certainly odd. I'm afraid my experience differs (after addressing a filament-on-extruder plastic friction point), and my printer sounds exactly the same with PETG and PLA (and ABS for that matter). I print about 50% of my prints in PETG, and I am able to sit next to my printer (in a lack enclosure) for several hours at a time.
Just a curiosity point: does the fan "whine" go away if you bend or flex the fan casing slightly in any direction? I was able to produce a mid-range (think middle-C on a piano) pitch by forcing the fan casing in such a way that the blower began vibrating or rubbing on something. If you find something like this, using an extra shim on one of the mounting screws (between the fan body and the printed part) may help twist the fan body back into a good alignment.
Edit: I listened so some of the videos posted on the github page linked above. When PWM is being utilized (i.e., fan is not at 0% or 100%) to control fan speed, my fan does indeed sound like what's captured those videos. I don't find in bothersome, and the sound is certainly a common characteristic of PWM controlled fans.
It's worth noting that the sound isn't related to printing PETG, except in that the filament type prefers something less than 100% fan rate. The way I read this post originally, it seemed as if PETG was directly the culprit here.