As ugly as racism is, there are plenty of real world examples to take from. For instance Segregation and discrimination. Rather than blocking the Warforged players actions, simply challenge them and make them part of the story, like PhilipPhilip says in his answer.
Though I would go as far as to make it a skill challenge or check, involving the party in defending the Warforged. It has the possibility of ending badly (they have to take the other magic train around the city) but you give the option of success, and team bonding.
Once they succeed they don't face that trouble again and pick up the image of being an adventuring party not to mess with in terms of racism. This reputation can set up lots of encounters in the future, and even gain the party some friends who don't believe in racism. Not everyone has to be racist.
Finally, don't use this as a one-trick pony to flog whenever the world needs some flavour, use it sparingly.
Edit; if you want inspiration from another setting, look at the Discworld Golems. Books to look into are: Feet of Clay, Going Postal and Making Money (they don't cover this issue in grave detail, but it is touch upon).