See original comment here: https://jira.atlassian.com/browse/JRA-23969?focusedCommentId=249903&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-249903

For what it's worth, if there's anyway to make it NOT throw an exception if the LDAP server sends a referral and you have to follow referrals unchecked, that would be great. Currently we have a primary AD that happens to have sub-domains. However the account we are authenticating against is in the global domain, and gets a successful response. The AD controller then tells Jira 4.3.3 that there's a referral (but we really don't care because we know it's in the global domain), and while other apps we have using ldap simply ignore the referral and continue, Jira decides to throw an exception instead of a warning.

Seems to make sense. If you say you don't want referrals, then you don't want referrals.