In another question, a good answer is given regarding how Snape shot down suspicions that he was a double-agent by explaining his opposition to Quirrell in the matter of the Philosopher's Stone. Snape didn't know that Voldemort was back (possessing Quirrell), and he was opposing Quirrell, not Voldemort. Snape was brilliant.
But it doesn't seem to me that this would also explain why Snape would stop Quirrell killing Harry Potter during the Quidditch match. In the movie, Quirrell tells Harry what happened and of course Voldemort's right there hearing it all from the back of Quirrell's head -- if he didn't know from the start, or perhaps even directed Quirrell's efforts to kill Harry in the first place.
Wouldn't Snape's defense of Harry raise a second suspicion that could not be as easily answered as the first?