Some important differences in Eberron to Traditional D&D is: 1. Grey Morality. Alignment has no presidency in determining a characters actions. For instance you have a NG queen who wants war so that she can attain the throne of Galifar, and you have a LE vampiric tyrant who wants nothing more than peace, and to rebuild his crumbled nation to splendor. You have a LG organization who almost completed a genocide against an entire group of creatures who weren't all evil to begin with. You could have a CE character who really is just a rebelious teenage punk, who likes to break minor rules, and cause mayhem, but could never kill anyone or cause anyone serious harm. Does he need to be punched? Probably, but he doesn't deserve to be beheaded or anything. He'll probably grow out of this phase anyway.
Another thing to keep in mind is that monsters aren't bound by traditional limits to alignment. For instance you could have a gold dragon who is a horrid, sadistic villian, while you have a red dragon who is a noble, kind soul with a love in his heart for all of the creatures in his domain. I mean a black dragon, and a group of orcs helped to save the world from cosmic horrors, and bound them to Khyber. Probably the only other race to sacrifice more to save the world than the orcs, are the Coutl.