When Macbeth kills Duncan, he is beginning his campaign to get kingship. However, look closely at his interaction with Lady Macbeth here. He is not interested in killing Duncan at all, but it is merely Lady Macbeth's urging that convinces him to take action. Looking at Macbeth's soliloquy in Act 1 Scene 7, he notes first that as his subject, he should always protect him and as his host it is his duty to protect him. Finally at the end of the soliloquy he admits
"I have no spur
To prick the sides of my intent, but only
Vaulting ambition, which o'erleaps itself
And falls on th' other" (1.7.25-28).
This shows that he notices that he has no motivation to go out and kill Duncan besides his ambition. There is nothing spurring him forward. In the rest of this scene, Lady Macbeth acts as this spur. Even after he kills Duncan, he is shocked and unable to finish planting the evidence himself.
In both cases, the men are visiting his residence and he is acting as a gracious host. A host should protect and shelter his or her guest to the best of his or her ability. With Duncan, he at least takes pause before killing Duncan. With Banquo, he doesn't hesitate for a moment. With Banquo, he operates much differently. First of all, Banquo started the play as his confidant, someone he shared a secret with (the witches). He betrays their close friendship. He deceives murderers into thinking Banquo is responsible for all their problems and the problems of their families. Unlike with Duncan's death, he never wavers about his plan. As a matter of fact, instead of working things out with his wife like he did with Duncan, he goes ahead and works alone keeping his wife in the dark on purpose.
This is also a murder that is to prevent some future generation of taking the throne from his family line rather than an immediate threat like Duncan was.