I don't see anything documented about how to conditionally control
   whether or not daemons should be started (as is now done by
   /etc/rc.conf).
   
   There should be some way of disabling daemons other than deleting
   potentially hard-to-recreate files from /etc/init.d ...


did you miss this section:


A new system should have the following attributes:
	[ ... ]
        * Control over a function via /etc/rc.conf (rather than
          via the existance of a file/link in /etc/rc*.d).


?


*nothing* depends on the existence of a script in {rc*,init}.d.
they may depend on the existence of other files (eg, /etc/exports).