Our instance of JIRA doesn't have the ability to synchronize users, the option is just missing from where I've seen it in other instances. Here's the allowed operations... are we missing something perhaps?
Allowed operations: [CREATE_GROUP, CREATE_ROLE, CREATE_USER, DELETE_GROUP, DELETE_ROLE, DELETE_USER, UPDATE_GROUP, UPDATE_GROUP_ATTRIBUTE, UPDATE_ROLE, UPDATE_ROLE_ATTRIBUTE, UPDATE_USER, UPDATE_USER_ATTRIBUTE]