Based on the last episode, c46 quote " execute them as if they were normal hollows". As for the rest of SS, I don't really think there would be a problem with the coexistence of shinigami and arrancar, as long as their swords have the ability to cleanse souls-otherwise they would be just as threatening as the Quincy (speaking of which, Ishida should have tipped the balance and destroyed the world till now, he's killed bagillions of hollows all over the world and everyone's ok with it...)
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