Idk. I mostly just kill the doctor and then everyone in town because it always bugs out every time.

You can get some good stuff from the shop run by Penny, and there's a doctor, but you can replace the doctor with your own if you need to. Penny's unique gear are irreplaceable, so if you really want them, you could buy them off her first, and then save Amelia.

Unique Staggering Combat Shotgun, Unique Combat Armor Helmet.

Justice is worth more than the life of a Synth Infiltrator.

Bonus Points for elimination of Amelia Stockton if doing a Railroad Playthrough.

My character couldn't justify the Nazi-like experimentation they were doing to humans and synths, so I killed the Dr and honored my contract with the mercenary (can't remember his name) and freed Amelia. My 2 regrets from this are not buying the unique items first, and returning to Covenant, only to be attacked (without any chance at conversation) and killing them all. I wish this had been one of those quests that offered conversation options with high charisma that would have allowed a peaceful resolution, or at least an uneasy truce. I wonder sometimes, if I had returned several days later, would the Covenant residents still be hostile?