We have very strict export controls on computer components, even for systems not much faster than the computer you are probably reading this on.
It's possible that the person processing the order simply didn't realize that it's illegal to sell these if they are going to an end customer in Iran without getting an export license. People who regularly deal with international sales should know this, but a new employee that had mainly dealt with domestic sales might not realize it.
However, 300 server boards is pretty noticeable sized order, so even if it was an accident, I would think that it would get noticed by a supervisor that these were going to the middle east.
It doesn't sound like this was a common practice, and it sounds like they were fined enough to doing this unprofitable even if the got away with it 9 times out of 10.
I suspect they are going to be even more careful in the future, and the Iranians are going to have to buy their motherboards through even more indirect methods.
According to the article:
".....The exported boards were controlled for national security reasons..."
I guess that is what helped my assumptions about 'secret' software along...lol. Let's hope you are right and there is nothing more sinister than greed here.