re #20: Well, now that you mention it, that is pretty much how English works. We like to verb. (-:
I'm skeptical about 'single' in conjunction with any gerund; several of the examples in #1 sound quite awkward, suspiciously like Euro-English. Any source that ends in .eu should probably be considered non-native and handled with caution. And in fact, just because you have a noun in German does not mean you should use one in English.
You could use 'single' in terms of designing cages, pens, enclosures, etc. but in reference to the animals themselves, I would be more inclined to use 'individual.' A single pen could in fact just mean that it's one pen as opposed to two, whereas an individual pen is one that is for a single animal alone.
If it's about risk of communicable disease, then 'in isolation / to isolate / isolated' if it's for an unknown or short period, 'in quarantine / to quarantine / quarantined' if it's for a longer, fixed period of several months? Quarantine especially may depend on a precise legal definition for a particular country and a particular species.
I think you're right that 'solitary confinement' does tend to sound more punitive, though if you were criticizing it as a harsh condition for social animals, it might be appropriate.
In any case, like Marianne, I'm inclined to use a verb such as 'keeping animals in individual cages/pens/enclosures.'
But if it's driving you crazy, give us an example of one of the overladen sentences and see if we can come up with any other ideas.