It is clear that after carrying out his assignment, the carefree, easy-going Goober is a figure of the past. Note how concerned he is about his friend Jerry defying the school and also the Vigils. When he tells Jerry to sell the chocolates, he is described as a completely different boy. Consider this description of him:
Jerry felt sad suddenly because Goober looked so troubled, like an old man heaped with all the sorrows of the world, his thin face drawn and haggard, his eyes haunted, as if he had awakened from a nightmare he couldn't forget.
He is clearly a transformed figure. Note too, how in Chapter 23, it is guilt of of what he did for his assignment and how Brother Eugene was "broken" by the experience causes Goober to quit the football team:
The Goober sat on the curbstone, his legs jacknifed, his feet in the gutter. He studied the leaves clustered beneath his feet. He was trying to find a way to explain to Jerry the conection betweeen Brother Eugene and Room Nineteen and not playing football anymore.
Clearly, the guilt of Room Nineteen has changed Goober into a young man who is aware of what he has done, but who is also aware of the "evil" as he describes it at the heart of the school that he and Jerry attends.