>>3166242He didn't really abandon her, he just freaked out. He was afraid to confront her about it.
You can call Shinji what you want, but he's just an afraid little boy. I've seen grown, adult men avoid others over less.
The whole point being made throughout ep24 and EoE with the two,is that Shinji sees Rei as this beautiful, comfortable yet still very strong waif - his good memories of her are challenged.
He doesn't want to think of Rei, whom he knew as a human and had all those experience with, as an Angel. That's why he freaks out in EoE, while his memories flash by like photographs being torn into pieces.
Keep note that all of these are explicitly scenes from Shinji's PoV.