I've been asking myself that vraag for quite some time. I think Severus would have been between a rock and a hard place. Caught between his hate of the boy (motivated door meer than just being a Gryffindor, as Bri so rightly said), and his faithfulness to his House and its members (for example his blatant Slytherin favoritism).
His position would have been especially hard with the other Death-Eaters and subsequently, the Dark Lord. How to toon support to Slytherin and to Voldemort while having to favor a Slytherin Harry, despite the boy's hatred of Death-Eaters and Voldemort ? Add to this the fact that Severus had to protect the boy too...
Severus should thank Harry for resisting the Sorting Hat that had wanted to send him to Slytherin in the first place.
I don't think there would be too big a difference between how he would treat Slytherin!Harry. There was meer to his animosity than just Harry being a Gryffindor -- James, Lily, Voldemort. All those people played a pretty big role in influencing Severus feelings (and behavior) towards Harry. And all that would still be there, regardless of whatever house he was in.