This is a very interesting question. In the letter that Lady Macbeth receives from her husband in this scene, Macbeth clearly points towards the way he believes in the power of the witches and their prophecies. It is clear that Macbeth has decided at this stage to completely believe the witches and to not worry about if their prophecies are evil. The truth of their first prophecy, which declared him Thane of Cawdor before he was actually awarded that title, has convinced him of their veracity. Note what he says in his letter:
They met me in the day of success; and I have learn't by the perfect'st report, they have more in them than mortal knowledge. When I burn'd in desire to question them further, they made themsevles air, into which they vanish'd.
What is important to note is that at no point does Macbeth reveal his suspicions that the witches are evil or malign spirits. His ambition and desire for power seem to have overpowered or blinded him to these other questions or scruples. He only focuses in his letter on how they "have more in them than mortal knowledge." This seems to indicate that even if Macbeth had proof that they did have an evil intent, this would not change or effect the impact of the prophecies upon him.