JCR-3691: Search index consistency check logs unnecessary warnings for repairable errors

Skip extra sanity checks for nodes that are to be deleted.
Also avoid the warning for the missing parent node of /jcr:system

git-svn-id: https://svn.apache.org/repos/asf/jackrabbit/trunk@1539030 13f79535-47bb-0310-9956-ffa450edef68