I really like it!
When you say he's going to a state school, that doesn't necessarily have to condemn him to having the pee ripped out of him just because it will be a state school. It depends upon the culture of the state school, probably influenced by the area it's in, academic results it has, type of parents sending their children there etc.
Imagine this:
"What's his name?"
"Ptolemy"
Scenario 1: "Ahh, I've heard that name before somewhere, a young man, an architect presenting a tv series...." It's a conversation starter, if you feel like it, you can go on to tell them more about the origins of the name if they aren't already aware of it or tell them why you chose it. If they show more interest, great, they may be intrigued, congratulate you on selecting an unusual name and ask you more. If they don't, or say they hate it, who cares? It will never be a bland name so it will polarise opinion.
Scenario 2 "Eh? What Tolemmeee? Whatzzat? Never heard of it before, where does that come from then?" They might not have had the benefit of a broad education and they might be genuinely curious to understand more.
If of limited interest or intelligence and it's obvious they just won't care or want to know more, just say it's a name with Greek origins, old family name, whatever. There are many Indian, Chinese, Middle Eastern names etc that have to spelt out today anyway. People are used to what they perceive as unusual names.
Scenario 3: Very worst case scenario - A thick and horrid individual encounter, they think that it's a made up name, "T-O-L-O-M-E-E-E-E" Whatever will they think of next, ha,ha, what a ridiculous name, I suppose it's like another one of those Princess Tiami, Heavenly Hirani or Apple names, what is wrong with a good old British name!" Racist undertones,you know the type, think they know it all, always bragging, but in all reality know very little. See the lighthearted side of the situation. Have a set, short, snappy reply in place in your memory ready for this sort of very rare but expected exchange. Chances are, they might either realise they're stooooopidly ill informed or it will all go over their heads. Why care what they think if they're not the type of person you want to talk to anyway? Just laugh it off.
Scenario 4 - Someone educated "Ahh, that's an underused name, the great and influential Greek astronomer....." Sigh of relief, you can chat, laugh about how some people are really flummoxed by the name etc. Chortle that you thought that naming him with it would automatically make him great at geometry. Oh God, you can see I'm not good at small talk.
You can even use the introduction of name as an intrument to distinguish the pleasant, interested and educated from the plebs less enlightened. Get it all over and done with in the first few mintues of introduction, yah or nay!
School tutors and receptionists (whether it be at surgeries, offices, etc)are used to odd spellings in today's world anyway. His friends will naturally just accept it. With Wikipedia, nobody is that ignorant anymore, anyone from the age of 7yrs old can type "Ptolemy" into Google and read about the origins of the name. It's not like the days of old when you'd actually had to go to a library and actively find a book that answered your query if you weren't fortunate enough to have been taught by someone who knew the answer or didn't own the appropriate books. The accessibility of knowledge has been completely transformed by the internet.
I would go for it! Look how much can be said about it! A lot more interesting than a top ten name.
Apologies for the long reply.