To be honest, I debate how much Shinji was actually trying to strangle her (at least in the sense that he was going to kill her) given that his hands are positioned in such a way that his thumbs both line up with her carotid arteries when every scene in the show previous to it had both hands clasping the neck with the thumbs wrapped around either side with one over the other (including the scene from the movie when Shinji strangles Asuka when deciding to initiate Instrumentality), suggesting intent to kill.
I almost feel like he was trying to feel her heart beat and to see if she reacted to test if she was even real. When she does nothing for what feels like several moments when he's doing something strange like straddling her and has his hands on her neck, he pressed down with his thumbs in a way that would cut off blood from those arteries and cause her to pass out before actually running out of air, suggesting he might be trying to do some kind of mercy killing because she's a vegetable or was desperate for a reaction of some kind. That, and the amount he trembles while doing makes me wonder if he was just desperate for some kind of response to make sure it was actually her and not an illusion or something (likely fully expecting her to reject him or react with anger like she normally would). Her caressing him was truly unexpected though, causing the break down (probably both from the shame of having initiated Instrumentality willingly once given the choice, their experience during it, and just having tried to choke her along with her actually accepting him and doing something nice). Her last line was excellent in regards to confirming she was still truly herself given the fact she just caressed his cheek, along with an appropriate reaction in general.
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I wrote a post about my hypothesis here,
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