Even though one can set -Dclojure.compiler.direct-linking=false, that doesn't change the already-compiled Clojure runtime, so currently it doesn't seem possible to disable direct linking there.
Disabling direct linking in clojure.core can be useful for dev-env-only tooling, that may e.g. improve backtraces.
I'd suggest that besides from the [org.clojure/clojure "1.9.0"] artifact, an additional artifact called [org.clojure/clojure-no-direct-linking "1.9.0"] is built/published.
I hope it sounds reasonable.