There is a check box to turn off the update notification, on the update notification. It doesn't get simpler than that. And turning off the update notification turns off ONLY the popup message, not the line in the statusbar. That cannot be turned off and it is not going to be turned off. There needs to be an indication that calibre is not running the latest code so that people have a chance to update before opening redundant bug reports.
I like the idea of making it gree instead of red, will be in the next update