I feel a little torn about the idea of losing wounded base defense. It was incredibly essential for piratez, otherwise I'd have no gals often, and despite the loses from system shock, it was more doable, since otherwise I needed to skip missions just to have guards "just in case".
I also understand your qualms about making it a percentage cut off, but this not only prevents unnecessary deaths, but seems more realistic. I FIGURE In bad enough states, people would just remain bed ridden as shooting starts.
I know its a bit much to suggest the change in addition to cleaning, but it feels wrong removing a feature that wasn't implemented ideally to begin with.