Do you actually use the ABE specifically, that part can be turned off (NoScript > Options > Advanced : ABE and then uncheck the enable checkbox) without stopping any of the other aspects from working.
I'm not a dev but looking very quickly at pihole it seems it serves an index.html file (https://pi-hole.net/faq/is-it-possible-to-change-the-blank-p...) in place of ad content, you might make that a link to /dev/null or just make it a blank file, and see if that works? I suspect it won't as the ABE is checking for the correct origin of content and pihole is spoofing the origin.