The tracking code does not need to be inside the <body></body> tags of a web page. Google recommends it as to reduce mistakes. If you put the tracking code inside the footer, google explains that some browsers will not execute the js.
Clearly all browsers execute the js inside the header block as this is typically where people put the Google Analytics code. So, why not place the AdWords tracking code in the header? On most websites the header is replicated on every page. Thus Google does not recommend putting it in the header as this could cause mistakes. The conversion code can only be on the confirmation page. The safest place for the code to reside, where it will be unique and get executed is in the <body></body>.
Having the tracking code in the header is never a problem for our Confirmation Pages. Why? None of the pages share headers with any other pages. Thus the code can go anywhere it will be executed. Including the header. Probably not the footer. Our script block is in the header. And that is okay.