Why do the other kids think he is gay? Do they even know what it means? My eldest DS1 is 9 and said the other day when his brother jumped on him 'oh that is so gay' I asked him if he knew what it meant, he sort of did so we then talked appropriately about it.
Do you think your son and/or his friend is gay?
I do think that your comment about parens not wanting their children to be gay and passing on homophobic attitudes is not entirely true. People are scared and wary of things they have no experience of and I am not sure that the subject comes up that ofter to pass down homophobic attitudes. But I am sure they are some that do, but in the minority.
My Dad was gay, but married and had two children, divorced when I was 25 and went on to have one male relationship. It's so hard to hear it from someone you love, but it does not make you homophobic. I think until you are in that situation you cannot say that you will just embrace it wholeheartedly without issues; but issues and opions about it do not equal homophobia. I did not instantly go 'wow that's great I am so pleased' it was tough as hell but we got through it together. He died 10 years ago and I am glad he was able to be who he felt he really was before he died.
With children, there is always something some pick up on, some point of difference eg: ginger, fat, freckly, having no Dad, crap at sport, geeky. DS 1 has a large hairy birth mark on his forearm and used to get teased about having a Dr Who baddie crawling up his arm, he used to get upset, but has now learned not listen and take in other people's nastiness.
You can only deal with how your son deals with the situation, not the bad/wrong attitudes of others. You can't change everyone and it is up to the school to deal with any sort of bullying whatever the subject. I also think 9 is a tipping point for many boys to start developing a sense of individuality and less of a follow the pack mentality.
The school need to do more about bullying is it is continuing. Address the bullying, look after your son and his needs, but forget the bigger picture of others attitudes, you need to concentrate all your energies at school and home.
Good luck.