Yeah, I'd like to eventually make them fully nude, but I'm going to take a break for a bit.
Yeah changing back Mileena's face is doable. The MKX one however would be a lot of work since I would that model, then do a whole bunch of texture edits to make it match the style of MK9. Probably more effort than I care for at the moment.
It's not a fix for a glitch necessarily. It was an intentional thing done by the developers for some reason (probably to reduce rendering of objects not on screen). If you use a free camera mod, you will find that the victim will disappear after a few moments. You can edit the fatality files to prevent this from happening. This doesn't always work though, as sometimes things get reset and it looks weird.
Also, I forgot to mention one of my favorite changes to the fatalities I made. Scorpion's alternate:
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