Adding "Delete" and/or "Mark as read" to mail notifications in Mavericks
There is a free app called Herald which does have a Mark As Read button which I have used for a bit now and I can recommend as a stop-gap.

I dug around some plist files to see if anything related to this already exists. No luck, sadly. I also sent feedback to Apple using the link grgarside provided, if others do the same it may actually result in something!