In fairness, Jay demonstrated the ability to throw magic fireballs around in spite of her shrunken size. If she was to be interrogated as a likely enemy, keeping her arms restrained would not be entirely unreasonable.

Of course, we then get into the question of whether treating her this way was justified

We, as an author and audience, have inside information. The hero of magic, "Jack" (Jay), is also the shadowy person. It's easy for us to side with Susan in this situation, but examined from Susan's perspective, and how much she actually knew, was what she did okay? Put in a way Susan would appreciate, would it be considered... "very Starfleet" of her?

(what we both like Star Trek okay)

I don't have a definitive answer for that, by the way. I'm just smugly asking the question before riding away on a very tall horse. 

An Alien Perspective

Also worth noting is that this game universe measures morality based on its own perception of reality. It literally has zero context for "this person has knowledge beyond this universe and is therefore suspect", rendering it completely incapable of comprehending Susan's justification for doing what she did.

In short, as far as this world's morality system was concerned, Susan was continually acting aggressive towards Jay for no reason whatsoever.