I think Inoda will not allow Asuna to have sex with Kirito, but until she gets pregnant. Like, after Inoda impregnates Asuna and the test result comes out and is positive, Inoda asks Asuna to have sex with Kirito for one time, let him cum inside, and later tell him that she's pregnant (very classic plot in NTR).But that would mean, that Kirito is still having sex with Asuna and I don't think Inoda would allow this. If there really gonna be pregnancy then it will be around the end of the game I guess, and the birth will probably be the ending. I don't know how Fujino will make the 9 months pass, my only guess right now would be sending Kirito off to american to prepared thing for Asunas arraval and to timeskip this for the most part, with some phone sex scenes in between.
Edit:
Well, another guess, considering the new update, Kirito could be dealing with the administrator or be taken hostage by the council for some time.
After that, Inoda again forbids Asuna to have sex with Kirito (Asuna using the excuse of protecting the baby to persuade Kirito), while between Inoda and Asuna they have "mild" sex regularly. This is written in the "pregnancy perks", where Asuna has sex with Inoda when she's pregnant as a way to take exercises and prepare for giving birth to Inoda's child.