He should be grateful that his teacher just told him point blank that she will not be able to rate him highly on organization and work habits. He needs to consider whether he can get a better letter from any other math or science teacher that he has had in high school. And yes, if there is no other math or science teacher whom he’s already had who could write him a better letter, he would need to work like a dog early in senior year, and then ask in mid October, 6 weeks into the semester, if one of them could write him a letter if he is planning on submitting early applications, in mid November if not.
Also, does something need to be done to address his organization and work habits? Organizational coaching? ADHD eval and meds? Peer support? Counseling intern support through the school? This may be your last chance before college to get him some help, if it is needed.