I contacted the Airlines and they confirmed e-visa will work, thinking about it; visa on arrival is independent from the airline, so even e-visa says you have to fly with Turkish airlines or EgyptAir, I can get visa on arrival.
During check-in with NileAir I signed a form that they are not responsible about any issue happen due to visa; which means sometimes people face problem and it is not 100% guarantee it will work.
After arrival at Sabiha airport, passport control was easy and they accepted the e-visa.
I am sharing this with you so people can see real example not just references from internet.