However, I think Harry's suspicions are ultimatley going to be warrantless, even though Snape kills Voldemort in Half-Blood Prince. On Page 651, Voldemort is speechifying to the summoned Death Eaters and he notes that not all are present.
"And here we have six missing Death Eaters ... three dead in my service. One too cowardly to return ... he will pay. One, who I believe, has left me forever ... he will be killed, of course ... and one, who remains my most faithful servant, and who has already reentered my service."
That final person is of course Barty Crouch, Jr., who guided Harry to victory in the Tri-Wizard tournament and turned the cup itself into a portkey.
The "cowardly" person has to be Karkaroff, who fled the Tournmant when his scar burned so brightly. He also rolled on as many as Death Eaters as it took to get out of Azkaban.
The "left forever" must be Snape. As a great occlumens, he'd have been able to get close enough to Voldemort to learn the most-guarded secrets (without his spying role being exposed) and when he spilled those to Dumbledore, do the most damage for the good guys. And in book 6 when Bellatrix interrogates him, his abilities as an occlumens would serve him well. Granted, she probably couldn't get into his mind like Voldemort could, but all practice beating a lie deterctor Costanza style is good.
Shells also noted another clue as to Snape's being a good guy. In her words: