I know a lot of people frown when you bring in wrestling comparisons but this one might be warranted. When Bret Hart was leaving WWF (at the time) to join WWC, he was the WWF champion. The agreement was for him to win on the PPV event in his hometown I believe, and then surrender the belt the next night. Vince however didnt want to risk having his champion, leave with the title. You can see how having the guy thats at the top of you organization, leave as the champ would not look great and weaken your own brand. So he ended up screwing Bret that night, to prevent this from potentially happening.
So from that stand point, having Khabib leave the UFC, the guy who just destroyed your poster boy and something millions of people saw him do. If he leaves, then it sort of weakens the future champions of that division at least for as long as Khabib is in the fans minds. It woudl also give more credibility to what ever organization Khabib goes to, its like well they got this guy who we know is a stud these other guys must be good fighters to.