They are lynching her because she is a dark elf. That is how drow were treated in FR. In bg1 you have to fight a Flaming Fist as well to recruit her. It makes perfect sense in the setting.
Kind of getting off track here. I think the Minthara thread
covers some of my criticism of the alignment system in case you want to discuss that. Anyway, while usually the alignment system can just be excused as a lazy way to identify enemy encounters; in this scene it became directly allegorical to racism in the real world. I can't speak for her introduction in BG1 because I don't remember it clearly enough. From what I've read though, the dude trying to kill her has an excuse though.
Neither situation makes you lose reputation though. You get a -2 rep penalty when she joins the party (it goes away when she leaves too) which is again representing the setting with drow feared and treated with suspicion, disdain and outright hate.
Fair point. I just remember losing reputation. That might have been the actual reason.
Bringing this back on topic, I like to imagine that the intellect devourer and I can be friends again after the prologue. Some people have cat familiars. Some people have cute squishy intellect devourers. lol.