Avoid problems with ratchet straps to fasten MTB shoes
To fix your existing shoes, I would either move where the strap attaches to the "tongue" of the shoe or where the buckle is fixed to the side of the shoe. The straps are designed to be replaceable ( as well as the buckles ).

I would take a closer look at your shoes, many Shimano models have small screws that fasten the buckle to the shoe so it can be replaced. If I am remembering correctly, they also have two sets of positions so you can place the buckle lower
on the shoe if you want. 

Even if this is not the case with your shoes, you should be able to move the position of the buckle using pop rivets. This is something skiers do with ski boots all the time, so if your local cobbler can't handle the problem, you might try a ski shop.