I just finished re-reading that as well. When I got to that part this time, I thought that maybe the scar didn't hurt because of Snape, but because of the proximity to Quirrell and Voldy. But that Harry would think it was Snape.
Yes, I think the definite implication there is that Quirrel’s back being toward Harry, Voldemort is looking straight at him...
Yes, that's the way I understood it as well. Snape was talking to Quirrell, and when Snape shifted his attention to Harry I can imagine Voldy/Quirrell shifting his attention as well to see what Snape was looking at, and causing Harry's scar to hurt. Harry though would have only seen Snape looking at him, associating the pain with him and causing him to mistrust Snape from the beginning.