Board Thread:Suggestions forum/@comment-25012056-20160611141212/@comment-25661985-20160611144122

"By the time of the War of the Ring, the Orcs of the Mountains though permanently depleted, reclaimed Moria but fell under the command of Sauron and Saruman. They were, for instance, amongst the party of Orcs that captured Merry and Pippin at Parth Galen."

- Tolkien Gateway

I think both Mordor and Isengard would assume that killing Gundabad Orcs is an action to oppose them, so it will drop your Mordor and Isengard alignments.