It sounds a lot like the issues Clojure has with Java 9 are to do with rather non-obvious assumptions it made about how the JVM works that are now broken.

For instance, Leinigen putting itself on the boot classpath to get faster startup time is really a hack to work around the problem that Clojure apps do way too much stuff at startup and generates very old bytecode forms that takes a lot of work to verify. If you want to disable bytecode verification for Clojure apps you could just use -verify:none instead of blaming Java 9 for changing the way things are loaded at startup, which has never been a guaranteed property of the platform.

Lots of complex apps and language runtimes have been making assumptions about things that were never guaranteed or even documented and will need adjustment in Java 9, but that's OK - the prior situation was never sustainable and a big part of why Java 9 is taking so long and is such a big effort is to get the ecosystem onto a more sustainable, supported footing. Creating supported replacements for Unsafe stuff is one such example but there are plenty of others.