The "karma" system isn't so much a religious thing as a means of measuring 'good' and 'bad' behavior in general. Just because karma is the word they used for it doesn't mean it's a religious thing. Lying, cheating, stealing, and killing are wrong even if you're an athiest. But depending on who you lie, cheat, steal from or kill, and for what reasons, it's ... 'flexible'
Also, the presence of witnesses isn't a karma factor; it's a local reputation factor. Think back to Fallout 2, where you could have a positive karma, and be "Idolized" in Klamath but "Vilified" in The Den. If The Den is full of slavers, thieves, criminals and drug-peddlers, gunning down a bunch of those low-lifes is kind of doing the world a favor (positive karma) but it won't win you any friends locally (reputation). If you repeatedly steal from a casino where the games are rigged anyway, you shouldn't lose karma, but you should lose local reputation when the corrupt owners catch you. Contrarily, if you steal the last of the water supplies from a desperate family and don't get caught, you should lose karma since you've pretty much doomed them, but not lose reputation with that family since they didn't catch you. Karma has been in all the Fallout games, and for that matter most role-playing games (in D&D they just call it Alignment).
Besides without post-doomsday religion we wouldn't have these fun-loving wierdos: Servants of the Mushroom Cloud, Children of the Cathedral, Followers of the Apocalypse, Church of Plutonius, Church of Atom, etc. Sorry, but it just wouldn't be the same without a chantry of glowing Oppenheimer-freaks spamming "Nrc nrc nrc" to themselves. Remember to wear your eye protection when you pray.