The answer (hours later) is to use:
AnnotationConfigUtils.registerAnnotationConfigProcessors(ctx);
After the beans definitions have been read, but before the context has been refreshed for the first time. This gets me what I want (constructor autowiring) without having to touch either my XML, or my Class definitions. It will also scale nicely (in the future I can continue writing XML and Classes just as above, and won't need to change anything. The final bit of code which worked was:
GenericApplicationContext ctx = new GenericApplicationContext();
XmlBeanDefinitionReader xmlReader = new XmlBeanDefinitionReader(ctx);
xmlReader.loadBeanDefinitions(new ClassPathResource("config.xml"));
AnnotationConfigUtils.registerAnnotationConfigProcessors(ctx);
ctx.refresh();