Lennie understands that hurting things physically lets George down, but he doesn't understand the ramifications of the pain he inflicts. If you or I were to do what he did as he did it (on accident), we would feel guilt, shame, disappointment, depression... our heads would be messed up for a long time, if not for the rest of our lives.
Lennie, obviously, is already messed up. But on some strange level, his brain is able to sense that this one is really bad. I think he is actually going insane during this period with the hallucinations of Aunt Clara and the rabbit. However, he is comforted instantly at the sight of George. This shows how incapable he is of actually grasping the power of what he did.
At this point, late in the book, Lennie is feeling extremely guilty. He feels that he has let George down.
He talks to himself about doing exactly what George told him to do, and that makes him feel better. But then he feels guilty. This is when he has the vision of his Aunt Clara. She is scolding him because he has been a burden to George all this time. He feels so guilty because of it that he tells her that he will go off and live in a cave so that he will not cause George any further trouble.
Lennie is in a state of distress, as he has just committed a murder, or in his words, "done a bad thing". But he also knows that George is coming to get him out of this situation, as he has for all others.
The fact that he asks about the rabbits and whether he'll get to tend them still shows he does not understand the seriousness of the situation, as does his being proud of the fact he remembered where George told him to hide if he got into trouble.