The Law of Conservation of Detail (TV Tropes warning) implies that an important character who is subtle and evil (or even just subtle) has a substantial probability of being the villain.
However, while that gives evidence that Quirrel is the villain, it doesn’t necessarily follow that the villain (the one that is Quirrel) must be Voldemort.
Why does Quirrelmort even have to be a villain? Sure, he was terribly evil in canon, and in the back story, but he’s obviously been through some sort of magical transformative process, and that he may have made him redeemable. Killing Rita Skeeter is a pretty substantial mark against him, but we have very little idea what his real goals are.
However, while that gives evidence that Quirrel is the villain, it doesn’t necessarily follow that the villain (the one that is Quirrel) must be Voldemort.
Why does Quirrelmort even have to be a villain? Sure, he was terribly evil in canon, and in the back story, but he’s obviously been through some sort of magical transformative process, and that he may have made him redeemable. Killing Rita Skeeter is a pretty substantial mark against him, but we have very little idea what his real goals are.
He just tried to kill an innocent man, so that settles that.