In any case, your disclosure not only affects the problems with the previously adopted (hereditary) solution for Hibernate, but also with your development as a programmer as a whole.
This is how I will do it if such a project is dropped on my lap and is in urgent need of refactoring or improvement.
It depends on the stage of the life cycle of your software and the time when you have to make big changes or stick to smaller ones. However, migrating in steps will be the best option in the long run.
Keeping the application written in Java in the short term seems reasonable, serious processing in another language will certainly violate acceptance and integration tests.
As Joseph suggested, take a step from Hibernate to JPA. It should not cost too much time. And from there you can switch the back-end to another storage method. Work to share problems. Choose any concept that works best, some prefer MVC, others can choose CQRS, and others love a different segmentation / separation style.
Since the JVM supports many languages, you can always switch to any of them or at least partially implement the functionality in more dynamic languages. This will solve part of the problem when you continue to encounter the "stupidity" of Java, while maintaining excellent optimization of the current JVMs at runtime.
In addition, you can configure automatic integration tests ... since the application, I hope, will never be launched from your IDE, these tests will give you honest results.
Note: I never trust my IDE to get dependencies correctly if the IDE has the ability to inject its own libraries into my build or run path.
So, briefly outline: small steps; lose Hibernate and move more abstractly to JPA; if Java becomes stupid, then gradually switch to a smart language. Your main task should be to rebuild the code base without losing functionality, bearing in mind an open design that will make it easier to add interesting and interesting functions later.