To me, it looks like bug 53631 has always been around. I know you said:
"my testing turned up Bug 53631 - cancellation doesn't close message window, which seems to be new in this ZCO"
but I just tried it in 6.0.8 and got the same behavior. So I wouldn't think this should be a reason not to deploy the special 6.0.9. I will do some investigation into this bug to see when this got broken or if it ever worked at all.