I just found the following; does it mean, that because I've already published my site, that I cannot save it as a template (the below references 2013, my site is in 2010)?
In previous versions you could still save a site as a template when Publishing is turned on by doing it manually. In 2013 Microsoft closed that loophole.
There is now no way to save a site as a template with Publishing enabled. The API will throw an exception as you have seen. It can't be done.