You don’t mention how you have tried to end the job. Have you used ENDJOB with OPTION(*IMMED)?
If so, have you also tried ENDJOBABN (End Job Abnormal)?
After the reorg of the physical file is finished, the RGZPFM command will rebuild all of the logical files attached to the physical file. Also, if you are allowing the users to change the file (Add/Delete/Update) while the reorg is processing you will add to the amount of time needed to finish the job.