Use command line to upload hex code to teensy.ex
This is starting to drift off topic for this site, but the best solution for making an automated programming utility for the Teensy on Windows, short of writing one yourself, would be to use some kind of UI automation framework to automate the process described in my earlier answer. My favorite one that I have used in the past is AutoIt. It has tools to inspect applications so that you can programmatically click buttons and fill out fields. There are even ways of having it run programs without them being visible to the user. There are plenty of tutorials on the web on how to use AutoIt so I would suggest googling for that. If you have further questions on how to do that, they would be more appropriate on a site other than Arduino.SE.