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.
Sign up to receive a 10-part series of useful information and legal advice about the divorce process.