I just wear my vibrams. If I'm going to hop in the saddle, I switch to something with a heel. If I don't switch back quick when I'm done, my back reminds me.
I haven't had any problems. My kids are all barefoot and I haven't been stepped on in years. They are the calm QH type. If I'm turning out my friend's high strung horse that does have shoes, I'm just extra careful.
I did get a pair of the hiking vibrams, I think they're KSOs or something, but usually I don't even bother to switch. Though i should, would save me washing my regular shoes every other day. Lol
the heel is only intended to help you from getting your foot caught in the stirrup, and many endurance riders ride in non-traditional footwear (aka no heels) plus wide-platform stirrups with a toe-cage (look up EZ rider stirrups for an idea).
why couldn't you ride in your barefoot shoes in something like that?
as to not getting your foot squashed when stepped on, well, I have no ideas.