For the record, I never did find a way to do this, instead I put a bit of code at the beginning of my script to look for an open version of the ActXServer, and close it.
if exist('xl','var') % Check if the server has been opened at all
if length(class(xl)) > 9 & class(xl) == 'COM.Excel_Application' % Check if excel is in use
xls.Save; % Saves the open workbook
xl.Quit; % Exits excel
xl.delete; % Deletes the variable