You can uninstall Structure from Plugin Manager the same way you uninstall other plugins. You can also manually remove structure JAR from
plugins/installed-plugins directory when JIRA is not running.
When you uninstall Structure plugin, Structure data is not removed. It remains in the JIRA's database.
It is perfectly safe to uninstall Structure plugin, then install it back again. (This happens, for example, when you upgrade to a newer version.)
All Structure data will be there unless you manually remove it.