It’s great he said that because now you have a teachable moment. In his journey to and thru adulthood there are going to be many times when he ought to have uncomfortable conversations and ducking them is seldom the best approach.
That all said, IMO he should ask someone else. I can’t imagine any scenario in which the teacher he already asked is not intending to give him low marks in the areas she mentioned, and furthermore she had the integrity to tell him that directly. A lot of teachers would just smile and say “sure”.
Every student asking for recs should ask the teacher(s) whether they can write a positive letter. In the book “The Gatekeepers” by a NYT reporter that shadowed the admissions committee at Wesleyan for a year is a real-world example of a bad rec. When the student asked for a rec she undoubtedly assumed it would be positive, but here is what she got:
There were times, I must admit,that I thought Tiffany might have taken a stronger interest in mastering the material in our course. When I saw that Tiffany was a National Merit Semi-Finalist I was a bit surprised. While clearly bright and competent, I had seen in Tiffany neither an exceptional skill for testing nor a particular affinity for the subject.
This could have been avoided if the teacher had been asked if they would write a strong rec. The student did not get in.