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1. Where does the powdered waste and eliminated enema liquid go?
2. How is the head screened for contaminants? Especially considering the hair, eyes, etc.
3. This sounds like a terrible thing to go through, but it also doesn't seem highly effective. How is it eliminating free radicals? How is it cleansing viruses and such?
I'd still like to have these systems on a ship like the Val'ta, but we need to have a less invasive option. What you're suggesting (which I know the influence of thanks to a Jim-shaped bird) is a human sandblasting. Are the facilities capable of a less invasive set of procedures if the threat is not severe? The life support systems should be capable of dealing with suppressing benign things.
By all means, we should have an intensive process in case of the worst, but we need this system to be able to deal with less severe problems too.
I would also like to point out that the suit that soldiers will be wearing is much more durable than the actual soldier, as such you'd probably do better at decontaminating them if you kept the suit on them (since you could subject it to much more hostile conditions that would more likely remove carried pathogens) instead of throwing away a powered suit every time they come back from a mission.
Enema liquid is incinerated and packaged but can be preserved for study.
The head is screened using the liquid system and resulting intraveinous liquid application.
Yes, its terrible but so worth it.
Free radials are dealt with using targetted anti-oxidants.
Viruses are detected during the quarantine segment, taking several hours to examine a multitude of blood samples. Most of the time is taken up by CPU overhead which is basically simulating the behavior of anything its unfamiliar with.
In all seriousness, the best decontamination equipment is an ST transfer. Anything else is just cheesetech. Tech that's cheesy generally lowers a player's sense of immersion or belief.
Having stakes is what creates problems. Roleplay is creating problems for players to solve that entertain them.