What are the drawbacks, if any, of killing everyone in Paradise Falls?

If you gain access to Paradise Falls the normal way - through the quest to enslave a few NPCs - then you get the chance to 1) Recruit Clover (one of the slave girls you killed) and 2) Continue enslaving NPCs (with the mesmetron) for caps. You also miss one or two minor sidequests, like giving the trader 10 Chinese Assault Rifles to expand his stock and caps.

But, beyond Clover, you will miss out on nothing major and if you feel like not being an evil bastard and working for slavers then certainly feel free to kill them all.

In most of my playthroughs I tended to sign up normally by enslaving the sniper who is hostile in the mined town north of Germantown then I recruit Clover, then I redeem myself by purging Paradise Falls :)