Hey Doug
I'm an e-learning advisor and here we combat the scroll of death in a similar way to what you're saying. You mention that your solution results in the resources being listed twice - once as an upload and once as a link. We've found a way around this.
What we do is upload the files in to a hidden section, BUT we keep the individual files unhidden. I think this doesn't work in IE, and you might have to switch browser and or AJAX on or off, but what this means is that your resources are visible and you can link to them through the links in the table, but it prevents them being duplicated