Jails don't HAVE to be places of cruel and unusual punishment, as they are currently in the US. The prisons in Norway, for instance, are humane - they almost look like real homes. The purpose of a jail is served (ensuring people can't harm those in society) while diminishing side effects as much as possible and encouraging rehabilitation. Example: http://www.globalpost.com/dispatch/europe/091017/norway-open-prison
Population/natural resource exhaustion related crises are a bit iffy, because it is plainly obvious that if they remain exponentially growing forever, relative to linearly growing or constant resources (like room to live on), one or the other has got to give. Mispredicting when it will happen is different from knowing that it has to happen eventually, and how could it not? Even expanding into space won't solve the problem, since the number of planets we can reach as time goes on is smaller than exponential population growth rates and demands for resources.
There are definitely plenty of other scientifically held views that get overturned here and there, though - another example is fever, which for centuries has been considered a negative side effect of an infection, but lately it's been found to have beneficial properties, as certain elements of your immune system function better when the temperature rises (and certain viruses function worse). http://www.newscientist.com/article/mg20727711.400-fever-friend-or-foe.html
In the case where someone wishes to commit a crime so they can spend time in jail, they'll probably perform something petty, which isn't TOO bad especially if they can confess and the goods be returned (or an equivalent). If social planning can lower the poverty rate and provide ample social nets and re-education for people in a bad spot in their lives in the first place, this thing is also less likely to be a problem (conversely, if more people become poor, prisons will be pressured to become worse to keep them below the perceived bottom line). Finally, prison can be made to be nice, but it isolates you from friends, family and all places outside the prison, and imposes routine on you, so if you desire control over your life you'll be discouraged from going there.