The answer from the IRS has been this: you only get the full $500,000 if you sell during the tax year in which you were married and filing a joint return. Otherwise, the tax code sees you as single, and then you're limited to $250,000.
Under WA rules you should not own the house together as community property or as H/W. I imagine your ownership is as joint tenants in common. She gets the $250,000 credit in her own name. You need to qualify for your own exemption which means that your expectation to pay capital gains after May 2009 is correct.
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