Shinji is just doing what he thought Asuka would want, given her last recorded communication with him "But, if I have to be with you, I'd rather die!". She indicates her fond approval that he has remembered. He bottles. She reacts with disgust.

It implies that Asuka is broken, beaten down, and just wants out, for everything to actually be over, rather than almost so; she has made the effort of will to leave the indefinite suspension of LCL, but appears to be physically debilitated - bandaged, and unmoving, but for one arm.

Given what last happened to her in the physical world, she is now bereaved, and her raison d'�tre (being a - the - EVA pilot) taken from her, everything gone that awoke her from her previous suicidal state, and having suffered the harrowing of Complementation, I don't think that this is at all unlikely a possibility.

At that point, rather than being a selfish cry for negative attention - the consensus opinion of why Shinji started strangling her - his act becomes one of twisted love, the sort of thing his Dad would be proud of; until, unwitting, Asuka's gesture Asuka touches Shinji's cheek reminds him of his mother's similar farewell.  Yui touches Shinji's cheek in a gesture of farewell.

The memory of that same gesture of farewell is a very good reason why he might then be overcome with emotion and falter in his resolve.

The idea that she is broken also gives a reason for her uncharacteristic passivity, unlike what might be expected if the Asuka/Shinji shippers were right. In that case, rather than speaking her disgust, it would be more likely that she would start a tussle (that might end in a clinch if the credits didn't start rolling).

And Asuka, knowing that he was capable of willing murder - having experienced it first hand already once - shows her disgust that he's not capable of doing it once returned to reality. Her nightmare has come true.

    Asuka:
    This sucks!

- a more colloquial rendition.

In that sealed reality where they were the only two people in that reality/world.  Sort of a similar theme too, Haruhi rejects a 'better' world for the current reality just as Shinji chooses reality over instrumentality.