Macbeth is upset because what he sees isn't a body--it's a ghost. He has seen and created many bodies, but this is no body. He says at one point:
...The time has been
That, when the brains were out, the man would die,
And there an end. But now they rise again.... (Act 3.4.78-80)
Banquo is dead, but apparently doesn't want to stay that way. This frightens Macbeth so that he once again behaves in the way that his wife repeatedly tells him not to: like he is terribly guilty of something.
In the end, she chides him for throwing another fit, and dismisses his antics, telling him that he looks on nothing but an empty stool.
Yes, but those victims he slayed did not get up again and walk towards him with an accusing face! He might have turned and run if they had - because of course that would have made them paranormal or supernatural beings! Who knows what 'super' natural other powers might they have! No wonder MacBeth was terrified of Banquo's ghost at the banquet in the play "MacBeth" by William Shakespeare because we know that people of that time were very superstitious and suggestible - as Macbeth would have been too. Don't forget the importance of the theme of the supernatural in this play - this scene is continuing the atmosphere from that involving the "weird sisters" - the witches.
In my opinion, this is because there is a major difference between killing in war, which is easy to justify in our value system, and killing for personal gain, which is pretty much murder.
Macbeth has, as you say, killed lots of people, but that was in war where it was expected and admired. Now he is doing things that are not expected or admired. It makes a lot of sense to me that he would feel guilty about killing Duncan and Banquo even if he could kill and kill in battle and never once feel bad.