I was under the impression that the warning was pertaining to the Asuna x Kirito romantic relationship. Not "This guy will work too hard" or "This guy will create fucked up shit", but "This guy lives in a different world to us".

Yuuki was telling Asuna that Kirito may not be someone she can accept or relate to in the long run.

The statement talks about what/how Kirito is, than about what he is about to develop.