This is actually a very GOOD point!You know the thought that Administrator replaced Yui really feels awful. If she replaced her, then she literally rewritten her. That means Asuna's nympho actions freaking killed her "daughter". That's fucked up on so many layers. Just rewritting her memories to think that her father is Inoda would be way less cruel than THAT.
So basically Asuna agrees to fuck Inoda because she has to complete the ritual otherwise Yui crystal will be broken.
BUT! If she fucks Inoda and finishes the ritual in this way, that "Yui" isn't Yui anymore! Even as an AI program, the new "Yui" relies on Asuna's and Inoda's game data, so she's no Yui, and Asuna must know this!
So it doesn't make any sense if Asuna, with a good brain, would want to complete the ritual with Inoda and let him be the father, because she won't get the true Yui in this way.
I understand Fujino wants to push the story forward, but there are just so many plot holes (just like this one) that make Asuna brainless (maybe she IS brainless).
So like what I read in the Chinese discussion community on this game: It's a good game if it helps you nut. Just don't think. The story doesn't make sense.