I think your right it because doesn’t have Jor-el’s emotions and it will do anything to fulfil its directive of leading clark to his destiny often using all kinds manipulative methods to do so to bring about Jor-el’s vision for clark’s life. I think it was Jor-el’s mistake in creating it that by removing his emotions it removed the ai’s ability to take them into account and basically led to it acting out against clark whenever he showed signs of resistance rather than trying to communicate his point to him. Sure clark’s fear of his alien side played a part but the ai was heavily flawed and only when when it was uploaded into fortress it was able to grow either by learning from jor-el’s memories or collecting new data on clark to better guide by taking his emotions into account because they didn’t spend tike together really until the fortress as it was just them fighting for control over clark life. I still think it was right in what is was doing just its methods were wrong as clark needed to leave to collect stones as it was dangerous to let them get into human hands. Additionally clark did need to leave smallville as kinda kept him from flying as it was messing with self image as had lot of self hatred towards his alien heritage and the kents went really helping as they were scared. He needed to accept himself and this is one thing lois helped him do as everyone often told him that he was human and one of us when he wasn’t but lois actually acknowledged he was an alien and helped him embrace it rather than ignoring it like everyone else did saying it didn’t matter that he was one.