i'd highly doubt that kotor would kill your hard drive. granted, this type of thing hasn't happened to me before, so i really wouldn't know. but that doesn't mean i can't at least try to help.
anyways, my first suspicion is that your hard disk was already on its last leg, and kotor 2 was merely a catalyst (with all the loading it has). now, i'm not trying to jump to conclusions, but how old was your hard disk?
as for the way kotor is running on your second hard drive, i'd need more detail on your computer (processor, video card, operating system, etc) before i can jump to any conclusions.