Eberron Alignment...
A minor quote: "Alignments are blurred, so thats it's possible to encounter an evil silver dragon or a good vampire. Traditionally good-aligned creatures may wind up opposed to the heroes, while well known agents of evil might provide assistance when it's least expected."
It still is on your character sheet. Holy Swords still exists, as do [Evil] and [Good] subtypes.
But, some things are missing. Specifically any spell effect or ability that allows you to 'read' or detect someones alignment. The Planes are different, none of them are aligned [Good] or [Evil].. so an 'Angel' may really have other things in mind. The Gods are not strongly involved in the mortal world.. you can be a Cleric of Dol Arrah, a [Good] diety but have slid treachorously away from the faith, but still able to cast spells, using your false faith to gain position and power while truely working for the Mockery.
Creatures, such as Gnolls and BugBears are relatively common in the cosmopolitan market places of the world. Even an occasional Troll bodyguard might be sighted with a delegation from the 'monster' country of Droam.
The world can be much more complex. Who is the Half-Elven representative from Cannith really working for? Herself? Some other faction?
Does your character care? More importantly, do your players care?
Eberron can be run with alot of political subterfuge and plot/counterplot. Or it can be a really cool place to run a straight dungeon crawl.
I hope this has in some small way answered your question