Kurt, you bring up many good points. I tend to avoid the campsites along the trail much of the time, but I do respect the area and try to LNT as many others have commented. As far as damaging the area, I take wide hammock straps to protect the trees, and if the ground is not clear, I don't generally make a fire. Needless to say, I'd always encourage people to follow the local rules with regard to designated campsites or no. I find that some of the sites are so used that they are packed dirt, the firerings have old bits of aluminum cans, etc.... They aren't terrible, but they're very heavily used as everyone hiking thru uses them. I pick a spot that's generally pretty 'out there' and very unlikely that anyone else will use for years, so the impact is very low.
Sounds like most of us are doing similar things.