IIRC it's deliberately done this way for a number of information security reasons. If you look through the gnupg manual, there are references to things like "on old systems, this program must be setuid root so it may lock memory pages". Presumably it's desirable to require such a thing in an isolated process rather than the entire application utilizing gpg.

Since quality CLI implementations must be provided and exist anyways, why not provide the programmatic interface (libgpgme) as a thin veneer over it, as if the commands are being run from the shell?