Its ridiculous really. The fact the NBA blocks the Chris Paul trade to the Lakers, but allowed KD to the Warriors is odd, obviously it was different because KD was a free agent, but the blocking of Paul to LA showed the NBA doesn't want super teams like this happening.
Apples to Oranges comparison.
While there was a definite conflict of interest in what happened with the CP3 deal, it was within the leagues power to do it. The trade certainly wasn't egregious and what the Pels were getting back was pretty fair.
The problem was that CP3 was the Pels only star player and the league was trying to sell the team. Losing him likely would have lowered what they could have gotten for the team.
The problem is that the league should never be in position of owning a team and on the exceedingly rare times that it happens, they should put a group in place to run the team and not involve themselves in the day to day operations.
In the case of KD to the Warriors, as you mention, KD was a free agent. It isn't within the leagues power to stop a player who has earned free agency from going where he wants to go. The league would have been sued and lost badly in court.
Plus, it took a perfect storm of circumstances, that we are unlikely to see again any time soon, to create the situation that allowed the Warriors to have the cap space to sign him in the first place.