No.
Although there were bigger plans for Shadow Who Walks I think it was always going to be a combat area. Mercs don't tend to like it when stangers walk into their secret bases after all...
http://fallout.wikia.com/wiki/Mercenaries%27_cave
Ah, so they renamed it. All I knew is that John Bishop got pissed when you talk to him after you kill the raiders (he even accuses you of being seen having a robobrain companion, even if you don't), so I figured if you talked to him first you might be able to help the mercs wipe out Vault City.
Given how obnoxious Lynette was I think a lot of players would have chosen this option.