How To Accept Payments By Check
A pure ghetto method would be to just go into the pdf template and remove the "paid" markup. 

I can't remember off hand, but I think it is just a div. Inspect the element to find the hook (id, class). Then either comment out the css rules or remove that element.

EDIT

It looks like this is the file you need to modify:

/craft/templates/commerce/customer/order.html