Scout thinks that it will be wrong to punish the wrong innocent man who does nothing wrong, just like a mockingbird.
Explanation:
Atticus had already told his children that mockingbirds are birds who do no harm to anyone or annoy anyone, rather they make sweet music for people to enjoy. So, when Atticus and Sheriff Tate were discussing about the murder of Bob Ewell, and that Boo Radley was the culprit, Scout references the mockingbird image to Boo and said that killing Boo will exactly be like killing a mockingbird, given that Boo is a shy and reserved person. (He also used to give gifts to Scout and Jem). So, the use of the mockingbird image is suggestive of the reference to innocent people who should not be harmed.
