From a narrative point of view, it's much more interesting to read about containment than destruction. A lot of the skips could just be tossed into an incinerator, and that wouldn't be fun to read about. Plus, it lends itself to exploration of ideas coincidental to the actual item in question, whereas destruction would 100% have to be concentrated around whatever item needs to be decommissioned.
In universe, it's the safe approach. Most things are unexplainable, the mechanisms behind them unknowable. But, their behaviour is observable, and so containable. The Foundation has a good couple of hostile deities contained, so the approach does work.