lucy24 - 4:46 am on Oct 4, 2012 (gmt 0)
if I leave these URLs as returning 403 status codes, will the Access Denied errors go away within Google webmaster tools?
No, but that's OK. From GWT's point of view, absolutely anything other than a 200 counts as an error. It doesn't automatically mean you did anything wrong or need to change anything. They're just drawing your attention to the situation in case you didn't intend for it to happen.
In some cases, a redirect may be appropriate. But only do it if you think that humans trying for /directory/ are looking for content that lives on some specific other page-- /directory/starthere.html, let's say.
I answered the Apache aspect of the question in the other forum.