The options in my.cnf are system variables. These variables are either dynamic (can be changed at runtime) or not dynamic. The ones that are dynamic, can be changed at run time with the SET variable syntax. You can see the variables with
SHOW VARIABLES;. But according to this link in the manual, the binary log option is not dynamic. So it looks like you have to restart. You might want to wait for someone who knows mysql a little better than myself to confirm this however.
Daemons in General:
In Linux, /etc/init.d/ holds scripts that start and stop daemons (services). Since these are scripts, you can view them with a text editor. Many of these scripts will take a reload argument. Looking at my mysql script, reload as an argument uses the mysqladmin command. So the manual for mysqladmin under reload says:
Reload the grant tables.
So looks like in general, this isn't for configuration changes, but rather changes in privileges (Maybe the equivalent flush privileges command? ).