Can I kill pedestrians?

You can drive over normal pedestrians, but nothing will happen. They don't have collisions and there's no penalty. They will simply keep walking, even inside your truck. However, pedestrians standing on the roads as part of the new random encounters do have full collision and act like walls. You can crash into them and it will damage your truck as if driving straight into a wall.

I have a mod which places pedestrians on the road and workers inside the loading areas. They can be driven through as if they weren't there, and I receive no penalty.

In theory this is a map-only mod, so the same is probably true for the vanilla ETS2 too.