That answer will contain spoilers from Alicization arc, which has not been animated yet.
Firstly, what Kayaba Akihiko uploaded onto The Seed wasn't his brain, not exactly — it was a copy of his "soul". As explained in the light novel: We have copied the Fluctlight of a number of test subject, and the Fluctlight is what passes through our neurons, so it's basically our soul. However, even though the process of copying somebody's soul is not risky for the real person, it is the case for the copies, because they will just "think" they were the real one and not just a copy. Most of the copies will simply cease to exist as they realize they aren't the original. Kayaba Akihiko's case was an exception, because his real self had already prepared to leave the real world to live in his own creation. So that's the major problem. Once Konno Yuuki realizes that she isn't real but just a copy, she would cease to exist.
The second problem is that the machine to perform the operation isn't public nor medical, and no one (except Kirito and a few others) knows of its existence, let alone where and how to do it.
In the Alicization arc of the light novels (especially the first two volumes of the arc), the details are much better explained than what I have here (they actually exaggerate with the explanation of pseudo-science, but well...), so I would recommend you to pick them up if you are into reading, as the Alicization arc is the best up to now in my opinion.