The easiest way I think for him to "fix" the scene for people who are upset would be just to change the dialogue, make Kirito a bit more conscious, he pushes Asuna down on the bed, before he puts it in she consents somehow despite not really being in the mood. That way you can still have the effect of her feeling pain from his "temp" big penis.Rape and pain was unnecessary, you could give him a big cock in FOG and he still would fail to pleasure her simply because he don't know how to use such a device, easy as that.
You could even keep the scene, make Asuna even excited about it, but in the end she feels near to nothing, same result, no rape needed.
Personally I had no problem with the scene, but if Fujino really feels like he should change it, I feel I'll be happy with whatever he comes up with.