Even if you develop a blister on the bottom of your foot, or a crack at the base of your big toe, you can continue to practice kendo without much difficulty if you know how to tape your foot up properly.
Here's a link to the Elastikon tape on Amazon: http://amzn.to/1zTwiCd
Standard dojo etiquette disclaimer: If your sensei tells you to do it a different way, please follow the advice of your sensei.