For Excel 2003-2007 files you can uncheck the "Check compatibility when saving this workbook" option in the dialog that pops up. This only applies to the specific workbook you're saving. But, that would be enough to get the pop up to stop showing up every time you go to save the file. You can at least work on one file in piece. I looked for this same option for .csv files but didn't find anything in the same vein.
If you're adventurous, you can try the Disable Excel Compatibility Checker plug-in over on Excel Guru. The author says it's pretty basic, only works with .xls files, and hasn't been tested all that thoroughly. But hey, might be worth checking out.