Nasu made it a point to say it over and over again, emphasize how it made her super horney, etc. Shinji kidnapping her at the same time doesn't help, as it's just another layer on heavy handed approach nasu took. Having Sakura angst about it is good, it's very reasonable for her to be ashamed/feel violated. Removing the majority of the narraration pushing it makes it a lot easier. Introducing it earlier in the VN would have helped spread it out, while HF could be left to go into the specifics.
- - - Updated - - -
A high budget 2014 anime looks better than an old visual novel is to be expected. I was mostly talking about her acting cute in my original post.