Your son sounds like a great candidate for home education. There are bound to be reasons why he doesn't enjoy school. The fact that those reasons may be more subtle than the reasons which make bullied kids miserable at school - so subtle that perhaps he can't identify them himself - doesn't make them any less valid. You don't have to know what the reasons are in order to recognise that school is wrong for him.
Can you do justice to his education? I think you are probably overestimating the difficulty of it, but maybe you would feel more relaxed if you keep an eye on the fall-back options in case you personally can't give your son the academic help he needs. You could try home education for the next 18 months and if it doesn't work, he could go back to school in Y10 for GCSEs. You could see what will be on offer at local colleges for when he is a little older. Some colleges do courses specifically for 14-16 year olds. Those are often aimed at less academic kids, but I do know several very academic teens locally who found these courses okay for them. Some colleges have fairly modest entry requirements for their post-16 courses, and you may feel that your son will have no trouble meeting those requirements even if he doesn't excel at GCSEs. Can you afford a tutor or two in key subjects? Are there local tutor-led GCSE study groups for home educated kids?
Start talking to parents in your area who are HEing slightly older kids and you'll begin to get a feel for how it might look for your own child. Many parents who are home educating at this stage report that the challenge isn't reallly about sitting at their kids' elbows helping them study. It's about doing the research and networking to identify the right opportunities in each subject: the little local independent art school, the fabulous online history course, the engineering apprenticeship. It's a big job, but you have a few years to get to grips with it. The sooner you start exploring that landscape, the more comfortable you'll become.
"He is naturally a bit of a loner at times and very attached to me, so I worry being at home with me wouldn't exactly encourage him to spread his wings!"
The great thing to remember is that there's no hurry. Your son may not be champing at the bit to go solo across the country on the train to spend a weekend with his mates when he's 15. Some teens don't even want to leave the house alone at that age. That doesn't mean he'll never want to leave you. I've known some home educated kids who were real "home-bodies", who didn't want to be away from their parents. Every single one has grown up to be independent. In this as in everything else, young people follow their own timetable.
I do think you're sensible to keep an eye out for opportunities for your son to make and keep friends. In addition to the ones you've mentioned, there will be opportunities through home education, since you say you live in an area with a good-sized HE community. Now is the best time to take action. It gets a little more difficult once they are a few years older, when many kids get their heads down with exam study and sometimes tend to stick with existing friendships rather than joining new groups. I found that older teens (mine included) weren't deliberately unwelcoming to newcomers, and if someone happened to get into their social group they were all quite friendly. But they were unfortunately a bit self-centred and didn't exert themselves to include newcomers in the way adults or younger children do. For example,
Teen: I fancy taking up Magic The Gathering again. I think I'll ask around to see who wants to do it with me on a regular basis.
Me: Shall I post it on the home ed email list in case anyone new wants to get together with you? We could hire a room, or you could offer it as an activity at the monthly home ed group.
Teen: Nah, I'll just ask my friends on Facebook. I know a cafe we can use which is really empty in the afternoons, so they don't mind us hanging around without spending much.
So it's actually easier for parents to promote new friendships when they are younger, less independent, and more reliant on their parents ferrying them around!
Give it a go. Trying home education is the only way to find out whether it could be the way to bring back your son's shine. He deserves to be happy.