You can resize the GUI using display_set_gui_size( 64, 64 );
Although you may have to run that code each time you go to a new room, GM can be very tempermental. :P
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Resizing the GUI works differently than resizing surfaces in GM, for whatever reason. The difference is that, as you describe, even after resizing it will still display subpixels (e.g. when you draw a rotated sprite, a primitive such as a circle, x/y positions that are fractions of pixels, etc.). To absolutely force the GUI to adhere to the pixel grid, you could instead draw all of your GUI stuff to a surface that's the desired size, then draw that surface on the GUI layer.