I -think- that the author could address this issue to some extent if he felt like it, but I don't know if he would do that, even for Blizzard.
For example, you could delay the logout/shutdown commands slightly using a hook and then let the system 'go dark' before finishing logout/shutdown. Another example: use the existing API to check that the user is in the right game before you send them a message.
But still, the author isn't the one to blame fully for the post-shutdown OQ spam - Blizzard bears a lot of that themselves since they didn't and haven't allowed those commands to be fired during logout. They should provide API access to versions of those functions that do not require a client acknowledgement, so that the author wouldn't have to use wonky methods to reduce spam for Battle.net, which isn't his concern anyway.
Still, I agree with you though, and I'm pretty sure oQueue will lead to strict limiting of this stuff in the future once Blizzard sees the detrimental effects it has cross-game. It's pretty much just a matter of time.
Edit in response to above: Cool, glad to hear it.