Could you please plan to integrate an option to turn publisher on/off in the next update. If you like I would be happy to provide the updated code.
In the following link google describes only using publisher markup on the most important page (usually your homepage).
The next link is in regards to authorship implementation, it doesn't actually specificy but given the way that authorship works it makes sense that you would want to include authorship markup on every page.
Given those 2 pieces of information the following blog (among quite a few others) makes the argument
"Implementation of rel=publisher should only take place on the HOME page of a site. It’s important to note that rel=author and rel=publisher will not function correctly if placed on exactly the same page. A good rule of thumb is that the rel=author markup is for content pages only, and rel=publisher is verification for your site as a whole (not needed on individual content). "
I hope to hear back from you. I will try to follow up with an updated pastebin for the added option.
Thanks for a great plugin!