What your GP should have done is reassured your child. You don't say what kind of thoughts, but age 11 isn't too young to have sexual thoughts. What is most concerning is that the thoughts are terrifying him. Why? What kind of thoughts are they? I got my first crush on a girl about that age, and pretty much every guy was having some sexual awareness at that age. So the question is, again, why is he terrified by them? That's the main issue. This issue of intrusive thoughts has been gone over on this website a lot, and my opinion, not shared by some others, is that this term is nonsensical. All thoughts come out of nowhere so all of them are intrusive. Why do we think at all? We're all full of thoughts. The problem is when those thoughts drive harmful action or make us miserable, and so the problem isn't that he's thinking but that he's terrified by thinking. If they're just the normal sexual thoughts people start getting as they get older, your doc should have told your son it's perfectly normal. Often that professional saying that fixes things. But if they are not the normal thoughts and are instead actually disturbing thoughts, that's a different situation and I don't see how an App is going to fix that. For that he needs to seek some counseling. Peace.
Does your son qualify to see a therapist? I'd start there. Is he a danger to himself or others?