This is just further proof that the government should not attempt to apply a one-size fits all heterosexual relationship contract for all sexual relationships. The situation can be easily remedied by treating all people equally under the law, pursuant to the equal protection clause.
Yes, the obvious answer to this whole issue is for government to get out of the marriage business altogether and stop subsidizing it implicitly through the tax code. The "nuclear family" is a fairly recent evolution in human societal structure and there's no reason to think that it will be with us forever and even less reason to think that it is the best way of organizing human society and should be preserved at all costs.