Body Flow Class Issue and Barefoot Revolution

I really am liking my Body Flow class, which is a mix of yoga, pilates and tai chi. However, I'm having major pain during the "standing strength" section, which is all about balance. My insteps hurt so badly, I have to stop. Would taping help? Am I doing something wrong?

I spoke to my instructor and, she thought I should just wear my shoes, but I'd really like to get into the "barefoot revolution". I'm saving up to buy a pair of merrell's. So I think I need to strengthen my instep? I don't know. I'd like some advice from the "hippie" people that like to do things more naturally, have a strong sense of yoga practices, etc.

Thanks much!