The most straightforward way to accomplish this is to include StationGlobals.ini in the workspace file that you are deploying. Of course, this too would overwrite the existing StationGlobals.ini on the target machine.
From what you have described, it sounds like Sequence File Globals may be sufficient for your needs. Sequence File Globals are global to all of the sequences in a sequence file. StationGlobals are variables that can be accessed by any sequence file run on a station. If you used File Globals, you would not have to be concerned about deploying an INI. The File Globals are included in the SEQ file.
If your system does require StationGlobals, the ideal way to handle this would be to have the StationGlobals.ini on your development machine have all of the StationGlobals needed by the sequence files on your deployment machine.
Now, to answer your question, you could use a sequence of ActiveX steps to have your additional StationGlobals programmatically added to the StationGlobals on the target computer. For example, you can have one step check if a particular StationGlobal exists. Then, if it does not exist, you can have a second step run that adds the StationGlobal and sets its value.
Attached you will find ProgStnGbls.seq that has two ActiveX Action steps. The first step checks for the StationGlobal. A boolean Local is returned by this step. The second step is the step that will, if needed, add the StationGlobal. This second step has a Precondition that checks the boolean Local. If the Boolean is false, a new StationGlobal is added. Then, a Post-Expression sets the value of the new StationGlobal. You would want to Run Main Sequence of this sequence file as a last step after deploying the test system.
Also, ProgStnGbls.seq is currently saved as version 2.0.1 of TestStand. It has been tested with version 3.1 as well.
Regards,
Eric M