thought it was pretty obvious that Rei, despite the gaps in her memory, was able to make the connection that of the two Ikaris, only one of them actually cared about her well-being and showed her any genuine human decency, and it wasn't the dude copping her tit like he owned it.
Hey! she was gasping in pleasure not pain.
I think that's just our wishful thinking. In EoE Rei's whole deal seems more of "I'm not a Doll." Then Shinji calls her. An interesting line was cut, where Rei thanks the Commander for his pure heart before answering Shinji's call.
In the series and EoTV though, it was a Rei x Gendo thing all the way. It was almost a "boy shows concern for empty girl, empty girl loves boy" anime cliche.