I was able to get what I wanted by manually editing the indexed colors array located in 'PHPExcel/Style/Color.php'. The array for the color set starts on line 371 for those that might be interested.
Not a perfect solution as now ANY spreadsheets generated with my installation will have the custom color set, but that shouldn't be a big deal for my particular setup.
I was not able to find any built in methods to set custom colors with PHPExcel, maybe that would be a good feature request? It would be nice to be able to set the indexed colors on the fly, and shouldn't be terribly difficult to add to the already terrific