Well, I can't comment about running barefoot, but I can comment about running in traditional running shoes vs. running in cleats. When I first started playing ultimate frisbee, I used running shoes because that's what I had. I got shin splits constantly. Within a week of switching to soccer cleats, with almost no padding, the shin splints went away and never came back.

It's also worth remembering that not everyone has been running heel first for years. Most of them haven't been running at all.