This is a wonderful metaphor and example of Shakespeare giving a character the language necessary to express the unexpressable. Just how affective would it be for MacDuff to enter saying something like "somebody just killed the king"? Not very.
Here MacDuff compares Duncan to a temple but not just any temple, ""the Lord's anointed temple ". In other words, Duncan was choosen by God to be king and that king has been murdered.
The murder of a king is an unnatural action, thus the "confusion". Look at the unnatual things that get reported about the night of the murder. Until the murderer has been brought to justice, the world will continue to be out of order, "unnatural".
This is important to the plot for that reason. The rest of the play shows us what happenes under these circumstances. People don't trust one another and begin to behave unnatually. When MacDuff goes to Malcolm, the young prince does not know if he is a spy sent by Macbeth, which is why he says the things he said. He is testing MacDuff.
Only when Macbeth is killed is order restored.
Don't forget, the Gunpowder Plot had only recently been discovered. There were always plots being hatched to kill the current ruler, so historically this was also relevent.