Thanks to the help of with Steve Maser, we found a solution that should allow to batch process files that refuse to open through a Double-click with the Service Pack 1 for Office 2008.

The problem appears to be related to the file Type and Creator.
Wiping out the file and creator for these files fixes the issue and allows you to open them through a regular double-click again,

There are several utilities that allow you to batch process files to wipe out the file Type and Creator. The first one that immediately comes to my mind is File Buddy. It’s a little bit on the pricey side for performing just this task unfortunately ($39.95).
FileXaminer can do the same thing and is a lot cheaper ($6). It can also run in demo mode for 14 days.