MSP-GANG programmer standalone script?
The user guide certainly makes it sound like your options are "standalone" or "script" and not a combination.. but your TI rep might have a work-around.

That being said I figured I would offer some suggestions based on some previous programming setups:

1) In the past, we would create a batch file to call the programming utility via command line. That way, the Contract Manufacturer (CM) just has to hit a button that says "PROGRAM FOR COMPANY X". If the concern is what the tool opens up in script mode, that might be an option. 

If the concern is your CM modifying the script, I wouldn't be super concerned. In general CM's want to minimize how much they mess with stuff, since any "tweaking" might result in a negative impact to their business. I would worry more about scripts getting mixed up and them having to call you rather than someone messing with the file.

2) Especially since we're talking about a company with an actual production process, it might not be a bad solution to just get two programmers in standalone mode and key /color-code / poka-yoke the crap out of it so they can't mix up the programmers. That way a technician can just hit the button on both programmers, and there's really no impact beyond having to plug in two cables rather than one.