I ended up not really making any changes to their reactions because my party ended up with days in-between their initial skirmish and when they actually went back (we had some lower-player count nights and so they went back to clear out some more of level 2 with their reduced party and I also threw the AV:X sword theft scenario in there because my players were getting a little worn out on constant fights) and I basically just ruled it that the ghouls pretty quickly got bored of waiting around on high alert and returned to their normal activity by day three.
But I agree it's a potentially serious issue on those floors with coordinated societies. A ghoul might want to get back to seasoning his meat with Blueblisters ASAP, but I'm not convinced that will hold true once they move past the arena.
That said, maybe the justification is that the way monsters are setup in the AP is intended to include their reaction to the players' assault. Like you normally wouldn't find ghouls hanging out in packs of four, normally they'd be out wandering around, reading random books, taunting the wood golem, warming up meat in the furnace haunt, etc, but with the players running around, they've decided there's strength in numbers and cluster together
