There is a distinct difference between "offering the victim emotional compensation" and "punishing the guilty", and there are fundamental reasons behind doing either.
"Emotional Compensation" is usually reserved for individuals if their lives are negatively effected by a crime. In this case, as a company, Apple has no emotional well-being, so it's hard to justify any claims that they need emotional compensation.
However, creating an adequate punishment for a guilty party is the very foundation of corporate law. The main focus of ANY trial is to try and ensure that a crime is not committed again. In a criminal trial, theoretically, you're trying to send the guilty party to a correctional institution (unfortunately, our prisons tend to do more harm than good, but that's a different matter altogether). For corporations, that means hitting them with enough of a fine that they take the whole issue seriously. The reason some corporate law suits sound so outrageous is that many times you can't possibly get results unless you hit a giant corporation with a hell of a huge fine.
The most disgustingly thrown-around case is that of the woman who sued McDonald's for being served a boiling hot cup of coffee. Most people read the headline, make immediate assumption, and deem the whole process corrupt. What they don't take into account is that the $1 million the plaintiff received wasn't because she DESERVED $1 million, it was because the corporation deserved to be punished $1 million in order to force them into compliance with the law. Where does that money go? If you retooled the system so that it went to the court system, then THAT would be corrupt... a non-profit third-party? Who's to say who gets what? The money has to go somewhere, so it might as well go to the one involved party that isn't part of the actual system: the plaintiff. That's why individuals often get enormous sums of money from law suits.
Why am I pulling up an individual's law suit as a way of describing Apple vs Samsung? Because the same concepts apply: Apple may not in-fact deserve $1 billion (although, in this case, they very well might, due to loss of sale), but Samsung sure-as-hell needs to be penalized a large amount of money in order to try and get them to not repeat their actions in the future.