I work for a company that writes software which client sites embed with < script language=\"JavaScript\" src=..... etc. etc. We depend quite a bit on document.write to wr
We've been using Jquery and set timeouts to rewrite code supplied to us by similar organisations to yours. Here's an example from Search Ignite:
The timeout has the added benefit of making our page responsive to the user before the the external code has been loaded by the users browser, very useful if the external supplier's servers ever go down. Yes we loose some tracking stats but the user experience is not compromised.
Obviously you won't be able to rely on JQuery but you get the general idea.