If you want more control over what is generated for individuals in your GEDCOM file, use your favorite genealogy program to export only the desired individuals and/or information about them. Or, use any of the widely available programs that change a GEDCOM file by filtering such information.
For instance you could use your genealogy program to create a report listing only living individuals. You could then export the individuals in that report to a GEDCOM file and then run GED-GEN.