Let’s discuss these two scenes. In both of them, Ward displays the same gesture - hands raised, palms open, in a show of peace. This man, tall and imposing, is trying to convey to Skye, someone much smaller than him, that he’s not a threat.
But in that first scene, he very clearly is a threat. He’s holding a gun in his hands and trying to make her believe that he won’t hurt her. He’s holding a gun in his hands and chasing after her and expecting her to trust that he means her no harm. And remember the context of this scene - Skye has just revealed that she knows the truth about him. Skye has just called the cops on him. He’s a desperate man resorting to desperate measures to complete not only Garrett’s mission - getting the hard drive unlocked - but also his own personal mission - keeping Skye safe. He is focused on himself, what he needs, what he wants and his tunnel vision is so strong that it really doesn’t register to him how threatening he appears to her. He truly does mean to protect her, but because he is so focused on what he needs from her, he doesn’t realize that he’s scaring her. He is so focused on himself - what will happen to him if he fails Garrett, what will happen to him if he loses her - that he doesn’t realize how much he’s pushing her away.
In the second scene, we see a dramatic difference. Yes, he’s in a prison cell so of course he’s harmless, but his body language is what really proves that to us. His whole demeanor is calm and unguarded, his hands are empty, and he actually takes a step backward. This little gesture is a huge piece of character development. It shows us that he really does understand what he’s done and how badly he’s hurt everyone around him. He’s been dying to see her, but he understands that she’s not comfortable around him and so he does what is best for her and takes a step back away from her even though all he wants is to get closer. This time, when he holds his hands up, it truly is a display of peace. It’s not just the barrier between them that’s holding him back - he is keeping himself at a distance because he knows that’s what she wants. In the first scene, he continued to run after her even though it was apparent that she was terrified of him. In this scene, there’s a moment when tries to ask how she’s doing, and she makes it clear that she won’t go there. And Ward immediately backs off, going back to the topic at hand and giving her what she needs - information - instead of trying to get he wants - a personal connection.
Remember that this man once tried to save this woman by force, against her will. Remember that this man was once unable to comprehend why she couldn’t believe that his feelings were real. And now, he keeps his distance, and now, he understands that what he wants might not be what she needs. Remember that Ward has nothing now. He has no leader to take orders from, he only has himself. And the fact that he’s trying so hard to connect with her, despite how cold and cruel and spiteful she is to him, proves that his intentions are sincere.
This is not a man trying to manipulate a woman into letting him out of his cell. This is a man who is trying to form a genuine human connection, possibly the first one he’s ever had.