The thing with Jordan's great 50% field goal percentage is that I don't think he'd shoot 50% if he played in this era of NBA basketball (late 90s to present). I don't think it's necessarily about the hand check rule or zone defense. I think it's more about Jordan's height, size, and strength for the shooting guard position in that era and the lack of emphasis on defense in that era of NBA basketball.
For much of the 80s and even early 90s, shooting guards were around 6-2 or 6-3 and 175-180 lbs. Jordan and Drexler were the new bigger, longer, taller breed of shooting guards. That gave them advantages in scoring on most nights. And, especially when Pippen joined the Bulls, it was difficult for teams to switch their small forwards to guard Jordan because Pippen would be able to exploit whatever smaller guard would switch on to him.
Also, defense has changed a lot since the time of the mid 80s to the mid 90s. It's not just zone defenses and the charge circles. It's strategies and emphasis. There were only a few teams like the Pistons and the Knicks in Jordan's time that played really tough, hard nose defense. You can see it in the FG% of a lot of players in the same era. Guys like Chris Mullin and Bernard King were well over 50% field goal shooters for their careers. Even less athletic, jumpshooting, smaller 2-guards like Jeff Hornacek and Rolando Blackman shot 50% from the field. In today's NBA, athletes are bigger and stronger and longer, they close harder on jumpshooters, have more length to bother shots, are more athletic, there are better coaching schemes. In fact, that's what makes players like LeBron and Wade (except for this season) so special that they're still able to shoot 47-50% from the field as perimeter players, although I do attribute it much to the fact that they attack the basket more than most perimeter players. But if you look at some of the other "great" scoring 2-guards over the last 10 years or so, like Ray Allen, Allen Iverson, Tracy McGrady, Vince Carter, none of them have been better than 45% from the field. It's a different NBA than when Jordan played, especially his prime years.
Now, that said, I still think Jordan would likely be a 46-48% field goal shooter, which would still be better than most 2-guards in the league, but I don't think he'd be a career 50% FG shooter and have seasons where he'd be shooting 52-53% from the field.