She is tender walking across such surfaces because we rarely traverse them in our regular training routine. If we did walk across these surfaces regularly I'm sure she would toughen up but that isn't the case. Hence, I would hate to cause a stone bruise or tear up her feet right before a barrel race.
Why do you need to boot this horse for such short distances? Exposure to rougher footing will only help her in the long run, by toughening up her sole. (This exposure is of such limited duration that I'm not sure it would help much... but I doubt it would hurt!) Is she really so tenderfooted that you cannot get her across these areas without boots?