Thanks for the clarification Loukas. I reviewed the relevant code, and there are possibly some tweaks we could make to the plugin, however given the multiple ways bulk updates can be made and the way auto publish is designed to be, well, automatic, there are some tradeoffs. Not necessarily tradeoffs in your case, but there may be in others.
Given that, I’d suggest the solution here is to just disable Auto Publish when you’re performing bulk operations. There’s no need to disable the entire plugin. If you’re finding that cumbersome for some reason, or someone else encounters this with TaxoPress, or some other bulk update method, circle back here and I’ll take another look.