My two kids did and still do the same thing occasionally. My son is 17, my daughter is going to be 15 next month. My son was always mature for his age, and my daughter was not. She irritated my son to no end, so he ignored her for a long, long time. I would not allow rudeness or cruelty, but I didn't make a big deal of it if they did not get along.
Over the past year I started noticing that if they were alone together, with no one around watching them, they actually got along and spent time together. I realized at that point that it was a temporary thing and they would be fine. They just both needed to mature.
Now they don't really spend time together because they have their own friends, my son has a girlfriend, but when they have to be together, they get along really well. That's what counts.
I think it will pass, and your son will mature and realize his sister is not as bad as he thinks she is.