Margin Holds: freight lines

We would like to implement margin holds on sales orders. We are discussing "by order" or "by line" etc. Our preference is to do this by line. But regardless, when freight comes into play, this could throw virtually every order on hold... even if we do the "by order" hold. How does the system get around this? how do other customers get around this? It would almost seem that this wonderful feature might be deemed useless if freight is ever charged on an order. Thoughts?