Keeping them out of the dirt is nice if you can do it, but skidding logs is pretty much the way most logs are handled. It isn't as bad as you make it out to be, but a lot of the end result depends on the circumstances, equipment, land type, weather (mud or snow or dry or??) and whatever else. Lifting one end of the log on the 3 pt and slowly skidding it out (being careful to move slow you you do not catch the log and flip the tractor over backwards) is a very decent and common method.
Basically everything Andy said was spot on. But the one point about flipping the tractor forward is not too likely. I'm not sure if there has ever been a tractor with a loader flip over frontwards. It's just not likely given the physics of it. If the tractor goes forward at all, the loader will stop it, pretty effectively.
Very not likely...
but there is probably one guy out there who had it happen just to prove me wrong 
. Tractors flip over back or roll over to the sides, they really don't flip forwards.
Watch your path closely for obstacles, work uphill/downhill as much as possible, and above all move slowly. The keys to keeping the shiny side up.