Perhaps could use a UnionFS for more transparency:
populate /var/run.vfs from scripts in /etc/tmpdirs.d
leave /var/run alone for packages that do put things there that should be in /var/lib
mount the VFS as UnionFS allowing normal write to /var/run
use Copy on Write for overwrites, store in /var/run.new
as /var/run should get cleaned on proper shutdown,
on boot before setup of the VFS move anything remaining into /var/run.old
(optional, but could be useful after a crash or compromise).

Just a thought.
-Z