Lathriel and
Kitanna,
Note that I've not heard anything regarding Bill's final demise or resting place; however, if you listen to the Directors' Commentary on FOTR EE DVD, you will hear that PJ et al wanted to do poor Bill in. At first I thought that they were joking, but as they droned on about it for a few minutes, I realized that they would have 'killed Bill' if not restrained.
One of my complaints regarding PJ is that in the ROTK EE he decided to add non-Book stuff (like the infamous drinking scene) yet couldn't show Sam reuniting with Bill - weren't the EE versions supposed to be for Tolkien fans like us?
If Sam could cry over releasing Bill, was the pony not then important enough for a 30 second nod in ROTK EE?