I think this is a dead thread, but I was just having this exact problem (after deactivating all my mods and starting anew). As I was reading this, Lokir started praying to the gods, and NPCs resumed their duties. Whether or not this will happen with every new game or not is a question mark, but who uses "new game" in lieu of "prisoner, nord, level 1" anyway? Point is, the solution looks like you just need to make like Axl Rose and use a little patience.