Another concern with a ghoul nest comes to mind... Retaliation.
Similar to a gang, if you simply murder a bunch of ghouls, someone may notice. Even if they were all feral (and especially if they weren't), the local ghoul community definitely knows the location of the sprawl's ghoul nests. Some other, less civil (and better armed) ghouls may some day show up. It won't be like a gang trying to scare you and make themselves look tough-- And it won't be immediate either. And those ghouls will ambush you, and might settle for just trying to infect you as well over just killing you. It's one thing if it's seen as an act of vigilantism or something, but if it's "we just massacred these ghouls because we wanted their crib", and you stay where it occurred, there's no way the ghoul community won't react to it somehow.
Maybe it won't be a serious threat to your livelihood. After all, you're professional runners with the resources to revamp this old nest into a batcave. But the point is it'll escalate and may not stop after one failed retaliation...