I don't disagree with your main points (although I think that Top 10 status is something that players, if not players and coaches as well would agree on), and I don't think they should do a league-wide jersey retirement or make Kobe the NBA logo, but you're also forgetting one thing: Michael Jordan was/is an asshole, and has been for decades. Chicago press kept a lot of stuff quiet back in the day but we all know many details that are off-putting to say the least. And we still don't know the whole truth about the gambling/"retirement" period.
He may have been doing some high-profile charity work as of late, but we can go back to his Hall of Fame induction speech to see what kind of person he really is.
Unless the sole argument is that the logo should be him because he's the best ever, he's also an "incredibly complicated person" who shouldn't be representing all that the league supposedly stands for. Just because he wasn't also a rapist doesn't make him an attractive logo candidate.
IMO, and I say this as a lifelong Lakers fan, it should be Bill Russell over anyone else.