Disable MySQL binary logging with log_bin variable
This is an old question, but it came up in a search while I was trying to jog my memory about the correct option name and so now that I've figured it out I'm adding the details here.
The key part of the question is:

I mean in an included file like /etc/mysql/conf.d/myCustomFile.cnf

You can do this from an included option file using the option skip-log-bin. E.g. you might create /etc/mysql/conf.d/disable_binary_log.cnf with the following contents:
[mysqld]
skip-log-bin

You can add skip- as a prefix to other options to disable them in this way too.
Related Q &amp; A: To clear currently accumulated logs, see this answer.