You could implement hook_theme_registry_alter() and modify the status_message entry to process through your function.
Thanks, that's exactly what I did!
@Nancy: I thought about submitting it to be part of utility, and I'm still happy for that to happen if you are, but the module as it stands is pretty hacky so I thought I'd better do a quick release so people can see it and I can get it fine-tuned.
Thanks to everyone else who commented during the discussion - if anyone wants to try and kill the module as it now stands, go for it - I'll be keeping a keen eye on the issue queue.
--Jim