Jaywalking is illegal in most (all?) US cities, but in many it's completely acceptable behavior. Jaywalking in Seattle (edit: was Manhattan), on the other hand is not done and you better not do it within eyesight of a police officer. Jaywalking in the Netherlands is completely fine (even right in front of the police), but in Germany it's not. The laws are the same, but the culture is different.
There are thousands of examples of socially acceptable behavior that doesn't correspond with the law. Drinking in public. Sometimes fine, sometimes not. Forging a signature. Occasionally fine, usually not.
Startups break laws all the time too. You have to get a product out first, and only when you start making money you get lawyers involved to make sure everything is going by the books. But if you aren't making real money yet the government really doesn't care whether you follow every law to the letter. And as a founder you have to decide which laws can be broken safely and which laws must be obeyed. Get it wrong and you may lose your company: either through legal trouble or because it doesn't get off the ground. The founders talk freely about the laws they broke. They brag about it! It's considered clever. Relentlessly resourceful. It's a fine line.
So if the culture in Harvard was such that cooperating for take-home exams was sometimes acceptable and sometimes not, then I consider that a legitimate excuse. It's easy to test too. Just look at the exams of that course of the previous years and check if people worked together on those too. Compare with other courses. If the results show that students consistently break the "individual work only" clause for some courses and not for other courses then the students probably didn't think they were doing anything wrong. They were just acting in the socially accepted manner.