Yeah... she was, effectively, using her own consciousness/soul (gem) to puppet Sayaka's corpse. If I understand it, Kyouko's justifying it to herself as maintaining the body against the hope of recovering Sayaka's soul and reversing the witch transformation — hence the eating (and excreting), since she doesn't have access to hospital-type IV support. (Ironically, Sayaka was the one with magic that could do that, if I get everyone's affinities right.)