From the pages os Mac OS X Hints.com get the most from X! http://www.macosxhints.com
Here’s a simple script to tell Safari’s downloads window to close.
Like I said, it’s simple. 
The on error bit ensures that it’s the actual Downloads window, not a browser window viewing a page with the title “Downloads,” that’s being closed.
If you’re running Quickeys or some other automation utility, you can set this script to fire every 5 or 10 minutes. If you don’t have Quickeys, you could also fire this script at a given interval using osascript and cron – see other hints for more on how to do that.
Unfortunately there doesn’t seem to be a way to check if anything’s currently downloading before closing, but for me that’s not a problem as I rarely use Safari to download things that take longer than five minutes.
OS version:
tell application "Safari"
repeat with w in windows
if name of w is "Downloads" then
set isdocument to true
try
set d to document of w
set the result to d
on error
set isdocument to false
end try
if (not isdocument) then
tell w to close
end if
end if
end repeat
end tell