But HAL didn't act "on a whim"! The reason it killed the crew is not because it went rogue, but rather because it was following its instructions to keep the true purpose of the mission secret. If the crew is dead, it can't find out the truth.

In light of the current debate around AI safety, I think "unintended consequences" is a much more plausible risk then "spontaneously develops free will and decides humans are unnecessary".

This is very true its the unintended consequences of engineering that cause the most harm and are most often covered up. I always think of the example of the hand dryer that can't detect black peoples hands and how easy it is for a non racist engineer to make a racism machine. AI safety putting its focus on the what if it decides to do a genocide is kind of silly, its like worrying about nukes while you give out assault riffles and napalm to kids.