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...all humans are around other humans who could kill them at any moment. Certainly any law enforcement of military officer with a sidearm has to be trusted not to shoot their comrades for not reason. Looked at like that is it so bad that Anna might be able to harm Hallie if she chose? One could equally say that the Shoggoth could melt Anna or G-Eyed could teleport her into the sun if he chose to; but they don't and they wouldn't.
The point really for all of Anna's problems is fear of technology. In this case, technology that's much more powerful than the average human. That paired with the fact that Anna's creator did something SPUD can't figure out makes them even more afraid of what she's capable of.