Deleting in favour sounds good. Do you know if gnome-applets is guaranteed (by virtue of depeds or recommends) to be auto-installed on an upgrade of a system which has command-runner-applet installed? If not, then perhaps command-runner-applet should be turned into a transitional meta-package which depends on gnome-applets?
Apart from that, a sentence about this should probably be dropped into future release notes.
