I hope that in Project Eternity, when you're doing something that might upset another faction, that it's not an instant deduction from your reputation but rather there's a reason for it.
This is a quote from the recent Wasteland 2 update
There is a small moment in the new Rail Nomads camp in which you hear a boy calling out for help as he is drowning. This time it would be a lack of action that could cause his death. Do you swim out to middle of the lake and save him or ignore his plea? And what happens when you are spotted ignoring his plea by a local resident? Do you shoot him before he can let others know of your behavior?
I am hoping that in a situation like this, that your reputation would only be affected if the local resident saw you and made it back to town to speak of the tale.
There are other ways around this though (magic, investigation) etc etc that could be used to explain away the reason for automatic reputation deduction, but it would be cool if you had the opportunity to exercise your ability to get away with stuff as well.