Is it possible to create a standalone exe which can burn the code into a Teensy 3.1?
Yes, it is perfectly possible.

You will need three things:


The HEX file you want to program
The programming utility for your chosen board (would be in the IDE folder somewhere - not sure what Teensy uses off hand)
A text editor.


Then, using the text editor, you create a .BAT file which executes the programming utility with the right parameters to program the board.

It can help to do an upload in the IDE in verbose mode so you can see exactly what command and parameters are being executed.