Hi,
For manufacturing level programming of the Kinetis, we recommend the P&E Multilink Universal tool for example the Cyclone Max tool, which support standalone programming.
As for the software, we recommend the PROG software which comes with a command-line programmer (CPROG). CPROG can be used to automate and speed up the programming process by running a batch file.
P&E's technical support staff can help you in getting the PROG and CPROG software to work with your setup.
Best Regards,
Fang