So don't use Hibernate if you are not an Hibernate expert?!
And don't expect to mix SQL and Hibernate operations freely in the same code, any more than you'd expect to freely mix e.g. encoding-aware String operations and manipulation of the underlying bytes. It's possible to make good use of the fact that Hibernate is implemented in SQL, CQRS-style: use Hibernate for your "live" operations in your application, use SQL for reporting/aggregation and ad-hoc querying, playing to both their strengths. But don't try to interleave them, especially in the same transaction.
People do this with SQL all the time; they see queries that aren't "fast enough" and they add indexes everywhere, or they "nudge" the query planner the wrong way, or anything else than to accept that maybe their data was wrongly modeled in the first place, or maybe they need to remove indexes, or actually, you know tune the DB.