What you are describing is a server plugin or extension. That way you expose your database via the REST API but at the same time you can access the embedded graph db hihgly performant from your custom plugin/extension code.
In your custom code you can get a GraphDatabaseService injected on which you operate.
You deploy your custom extensions as jars with your neo4j-server and have client code operate over a domain oriented restful API with it.
// extension sample
@Path( "/helloworld" )
public class HelloWorldResource {
private final GraphDatabaseService database;
public HelloWorldResource( @Context GraphDatabaseService database) {
this.database = database;
}
@GET
@Produces( MediaType.TEXT_PLAIN )
@Path( "/{nodeId}" )
public Response hello( @PathParam( "nodeId" ) long nodeId ) {
// Do stuff with the database
return Response.status( Status.OK ).entity(
( "Hello World, nodeId=" + nodeId).getBytes() ).build();
}
}
Docs for writing plugins and extensions.