We don't have any plans of supporting any additional sprite sheet import options for the reason mentioned below, but you can always use imagemagick to batch rescale multiple directories of images. Once you get your workflow sorted there, it becomes pretty stragihtforward.
The reason you don't want to rescale the atlases is that if anything in your atlas starts at a position that isn't perfectly divisible by two, you end up with pixels filtering incorrectly. This is made worse when downscaling 4x, as everything would have to align to a multiple of 4. We can enforce whatever is necessary when reconstructing the atlas.