Macbeth does not want to kill either of them, but he has to in order to become and then stay king.
Macbeth says that to be king is nothing unless he can stay king. He is worried about Banquo because he was there when they both heard the prophecies, and might suspect Macbeth. He is also concerned because one of the prophecies said that Banquo’s sons would be king.
Tis much he dares,…
He hath a wisdom that doth guide his valor
To act in safety. There is none but he
Whose being I do fear; and under him
My genius is rebuked, as it is said
Mark Antony's was by Caesar. (Act 3, Scene 1)
Macbeth basically is saying he does not want to kill his friend, but he is going to do it because he has to in order to keep his position. He similarly was undecided about Duncan. He chose to kill him after a long soliloquy in which he tried to decide.
This even-handed justice(10)
Commends the ingredients of our poison'd chalice
To our own lips. He's here in double trust:
First, as I am his kinsman and his subject…. then, as his host,
Who should against his murderer shut the door (Act 1, Scene 7)
Duncan did nothing against him. In fact, he was his host and cousin and should have protected him. Banquo was his friend. There was no reason to do anything to him either. Yet Macbeth wanted to remain king, and both were sacrifices that had to be done in order to secure and hold on to his position. It became the only thing that mattered.