You can exclude disabled users on User Profiles service level. Please review this article.
By default, user profiles don’t have “userAccountControl” property mapped to AD attribute. Theoretically, you can try to set up this mapping manually to use this filed in Org Chart filtration rule. Note, in this case you may need to use JavaScript bitwise operators to work with userAccountControl value correctly.
Org Chart searches for every user profiles by default. It is by design. if you want to exclude someone from search you need to use filtration rules.