Maybe I'm misreading the question, but you don't have to switch to hbm mapping completely.
You could continue to use fluent NHibernate to map classes and use hbm for named queries only. In your configuration, you'd then include the entities and the hbms.
_sessionFactory = Fluently.Configure()
In your namedQueries.hbm.xml you then only define named queries:
<?xml version="1.0" encoding="utf-8"?>
from SomeEntity e
where e.Property = :propertyValue