Simplest would be what you suggest to flip the axles and then use the higher mounting hole. If I understand your concern, the side of the spring would rub against the hanger bracket...but from the picture, I can pretty much guarantee that's happening already as you go down the road, so the upper hole shouldn't make it any worse. On the positive side, being closer to the frame should make the hanger stronger against side to side forces.
But really once you go thru the hassle, I would just do the flip by itself and try it for a season. You can always change the mounting holes later.
Another option if there is enough room in the wheel wells is to mount bigger tires. You could probably pick up an inch or two that way with no other modifications.
If you want to throw money at the problem, you could add airbags with a remote air fill compressor connected into the cab. Any time you are worried about clearance, just pump up the bags then release once you are back on the highway.
