Noticed this thread a bit late.
I've fully integrated warforged into my FR game - here's what I do (this is off the top of my head, based on my campaign material):
IMC, warforged were created (through arcane, golem creation-like methods - though their sentience was originally a mistake in their experiments) in Halruaa some hundreds of years ago, as a defence against the Arkaiun invasions (especially when the Arkaiuns sailed right up the gulf of Halruaa).
They are still fairly rare, though, and are used as special shock troops and independent scouts. The Halruaans now value the sentience of the warforged for their independent thought, though there is still unresolved debate to this day regarding the ethics of 'building' these sentient creatures. At least one (extremely powerful) wizard family/guild continues to build them against the regulations of the ruling power. Some warforged go rogue and desert the military/country, but this is considered as acceptable losses considering the warforged versatility (though not specifically "hunted down", they are considered fugitives just like any other army deserter). Depending when and how they were created (and by who), many are 'civilians', and work as bodyguards and the like.
(It's got a mix of Eberron backgrounds tied with FR history and locations.)