Alternative to going barefoot?

I am a cross country runner who trains without shoes because it makes my shins feel better. Recently my coach told me the athletic director said we have to wear shoes on the team. There are no rules in the handbook that say anything about this. Should i ask the ad about it? Or are there any suggestions for something else to wear? And please don't say wear big, cushioned shoes because i have tried a bunch of different models that were supposed to correct the problem.