But it wasn't taken out of context. It was recontextualized. Those are not the same.
As much as people go on about the importance of the meta level when looking at Rebuild, i think that in some cases it can be counterproductive. And not just on the level of personal enjoyment, but even when it comes to understanding the plot. For example, another scene that was recontextulaized is the one where we can see Gendo looking at a naked Rei floating in a tank. Everywhere i looked, this forum included, people, probably myself too on occasions, described that scene as "Gendo watching Rei at the Dummy Plug plant". Even though there wasn't even the vaguest of hints dropped that Rei has anything to do with the Dummy System in Rebuild's continuity. In fact, if i recall correctly, it was implicitly hinted that the D.S. was contructed at another base.
However, there is a scene which gives Rei-in-a-tank context within 2.0 itself: the aquarium scene, where she compares herself to fish in a tank that couldn't survive in the outside world. It's a much more obvious connection then anything having to do with the Dummy System, yet for a good number of people, meta level knowledge of the original canon overrides what is there before their eyes.
2.0 is a very sneaky movie this way, because it reuses a lot of scenes and imagery from the series, but that's just as distarcting as it is nostalgic.