I always like to have both files since the gcode is much more readable and can easily be ported to other machines in the future that have different x3g settings. But if you really wanted to delete it, you could probably setup a "command for post-processing" to do it (on the Scripts tab). Those are just terminal commands that run after the files are created. So if you were on Mac/Linux, you could just put:
rm [output_filename].gcode
The [output_filename] variable gets replaced with the name of the file you export. So if you saved test.x3g and test.gcode, then [output_filename] would be "test".
You may have to add a full path before that command. For example
rm /Users/username/Desktop/[output_filename].gcode
But I think you get the idea
