Running away when he approaches is not kind behaviour. It's understandable that he doesn't want to put up with the annoying quirks, but he needs to find a better way of dealing with the problem.
My dd was in a similar situation with a girl at school when she was in year 7. The girl in question was not an unkind person but she had a number of behaviours that the other children found incredibly annoying. Most of dd's friends just wanted to avoid/exclude her. DD was concerned about this because she knew it was unkind. However, she found it very stressful being around this other child, and she was also increasingly under pressure from her other friends to stop asking them to include the girl.
In the end, dd decided to talk to the girl directly about the behaviours which she and her peers found difficult e.g. excessive boasting, whining when she didn't get her own way, describing other people's beliefs/customs as "weird", tuning out of conversations and then getting in a strop because people wouldn't fill her in on the bits that she had missed. She had a very open and honest but sensitive conversation about the fact that she wanted to be friends with the girl and recognised her many good qualities but really struggled with some of the behaviours. The girl cried and said that she didn't realise she was doing these things. Eventually they came up with a code word that dd could use to make her aware of when she was doing it. There wasn't a dramatic improvement overnight, and several years later, dd still finds the girl annoying at times. However, she did take dd's feedback on board, checked herself when dd used the code word, and over time, she gradually became more self aware. This also helped her to develop other friendships.
It wasn't easy for dd to have that conversation, and it would have been a whole lot easier for her to have walked away, but actually, addressing the problem kindly was probably good for dd's own self-esteem as she learned that she could be assertive about her own feelings without being mean to anyone. About a year after she had the conversation, she received a really lovely card from the girl in question, telling dd how grateful she was for her honesty and her patience. The girl had been aware that other kids disliked her, but it seems that she hadn't really understood why.
I don't think it would be an awful idea to talk to the mother about what's going wrong for her son, because ultimately, he needs to know. Be prepared for the fact that she may be very defensive though. If your son can talk directly to the boy in question, I suspect that that would be much, much better - if he is able to do it kindly and sensitively, of course.