Unfortunately, nothing can be done about this. (Besides replacing all KDEish applications. But it was decided against that in this thread: https://forums.whonix.org/t/updating-whonix-from-jessie-to-stretch-migration-to-gnome-shell-port-to-gnome-ish-applications.)
It’s due to Debian package dependencies. It’s explained in this thread:
https://forums.whonix.org/t/uninstalled-vlc-completely-broke-whonix-can-i-recover