I just had a similar rkhunter report:
Warning: The command '/sbin/chkconfig' has been replaced by a script:
/sbin/chkconfig: a /usr/bin/perl script text executable
this hapened while I was still setting up the serevr, I remember, I couldn't find chkconfig, had to look for the package containing it and install it. would rkhunter --propupd remove this warning? I am sure that was me who caused that warning...