In DD it was fairly easy to steal or kill non-protected NPCs without getting caught, so the difference with reputation in BD is not that much in practical terms. I was a little disappointed that in BD you could loot an NPC's belongings without getting a reaction. From what I understand, that is a consequence of adapting the DD character AI so opponents had better tactics, so I don't mind the trade-off.
Hopefully DD2 will have a more elaborate reputation system, with consequences that effect the plot (though that requires a lot more work and makes things a lot harder to test).