In agreeing to Snape's request, Voldemort was operating on the assumption that Snape wanted Lily for his own. "He desired her" is the explanation Voldemort gives Harry in DH. Likely Voldemort presumed that, with James dead, Snape would attempt to convince Lily to marry him. Hagrid tells Harry in The Sorcerer's Stone that Voldemort had wanted James and Lily on his side. Hagrid isn't the most precise person on earth, but if that statement is correct, Voldemort may have hoped that if Snape succeeded in his relationship with Lily, she would join the Death Eaters.
Obviously that scenario is very unlikely. Even Snape, who doesn't have the greatest social skills on earth, never seems to have thought that Lily would renew their friendship if James was out of the way. Aside from all other reasons, their friendship broke over Lily's aversion to the Dark Arts before Lily even started going out with James. She would hardly befriend the adult, Death Eater Snape after his master had killed her husband and baby. But Voldemort may not know the exact circumstances of Snape and Lily's estrangement, and--more seriously--he does not understand love. It eludes him entirely. His misunderstanding of love is why he never realized that Snape cared about Lily as a person, not merely as a potential romantic partner. So he would not necessarily understand that a normal person would want nothing to do with someone who had murdered members of their family, no matter what personal gain they might receive. Voldemort operates strictly on a cost/benefit basis, and he has a tendency to assume that other people function in the same way.
It is possible that he may have also seen Lily as less of a threat than James since she was Muggle-born, while James was a pureblood. But, however Voldemort may have felt about Muggle-borns, I doubt he would have allowed prejudice to cloud his understanding of Lily's abilities. (For instance, he marked the half-blood Harry, not the pureblood Neville, as his equal. Pureblood fanatics like Bellatrix Lestrange or the Malfoys would have been more likely to assume that the pureblood child would become the more talented. Voldemort knows better, whether he admits it or not.) In any case, one look at Lily's school record--excellent student, Head Girl, member of the Slug Club--would have made it abundantly clear to Voldemort that Lily was not someone to trifle with. In telling her "Stand aside, you silly girl," he is probably not referring to his evaluation of her magical competence. Voldemort operates on the basis of cold logic. He would never risk his own life to save someone else, and he considers it ridiculous and illogical for Lily to do so.