I think the corruption is responsible because even as Horde you actually free those NPC's gang-pressed into service. Those are not vendor NPC's "defending their home," they're very obviously being pressed into a combat role, and when you kill their Kor'kron overseers they run off, they're not there to fight on their own recognizance. The rest of the vendors have their abodes boarded up or blocked off, protecting themselves from the Kor'kron and not from the PC raid bursting into the city. Y'Shaarj's influence probably amped up whatever feelings these NPC's were having that led them to join Garrosh to begin with - sentiments of Orcish superiority, hatred of the Alliance, etc. etc.
I mean in the very midst of being invaded the Kor'kron are conducting purges on their own down in the Cleft of Shadow, which makes zero sense when you're already under siege. But if you're talking about people who are being driven by external corruption it does make a degree of sense - they're not thinking properly, their passions being stoked to insane heights by the influence of Y'Shaarj.