There are upsides to this approach. Coupling Swift's AST with Clang's AST will allow for the best codgen, for sure.
However, the huge downside to this approach, which cannot be overlooked, is that Clang (not libclang) is not designed to be a library. It doesn't have the backward compatibility of a library. Swift (i.e. Apple) is already deep into developing Clang, and so I'm sure they can afford the cost of keeping up with the breaking changes that happen on every Clang release. For a solo dev, I'm not yet sure this is actually viable, but I will give it more consideration.
However, I think that raising alarms at C++ codegen is unwarranted. As I said before, basically any query builder or codegen takes some form of string generation. The way we make those safe is to add types in front of them, so we're not just formatting user strings into other strings. That's exactly what CppInterOp does, where the types added are Clang QualTypes and Decls.