How quickly Zelda recoils and scrambles away only serves to emphasize how bad her present state is. She's fueled purely by a fight or flight instinct right now, the former seeming to be prevalent given that intent to attack. What attack, Kratos neither knows nor cares. If it had come, then he would've reacted accordingly.

Instead, Kratos holds his former kneeling position, resting the outstretched arm on his knee which isn't touching the ground. He watches silently as her panicked gaze takes in him and then her surroundings. Giving Zelda a moment to process things also allows him to observe her in turn. The appearance is different (irrelevant), the reaction to him is extreme (concerning), and requiring to look around indicates not realizing where she is (also concerning). What had happened to her to cause this??

Only once Zelda tries and then fails to form sentences does Kratos speak, his voice soft and his gaze gentle. "You're safe here. No harm will come to you." There lies an underlying implication of him making sure of that.