We are currently relying on Hibernate to auto-create the database. The problem is that indexes won't be created

There should be database scripts for the KIE server. (see "Update:" below)
For example these are for version 6.x, https://access.redhat.com/documentation/en-us/red_hat_jboss_bpm_suite/6.3/html/administration_and_configuration_guide/ddl_scripts

consider the following:

• Have a config map with the scripts, mount it
• Create an init container for the database pod, or use the hook (or something) action to populate the database
• Make sure DB is not marked as ready till all this is done, otherwise we risk a race condition and Hibernate may also try to create the schema.

Update: Per the comments below, and a call where we talked about the issue on 2018-07-10, it has been decided that using JPA 2.1 annotations such as @Index @ForeignKey on the entities is the approach we should be taking, instead of using DDL scripts.