I'm assuming here that the OS already doesn't have the ability to suppress the popup, and I think that's a safe assumption because Apple doesn't want to have this ability.
how do we know that the iMessage protocol doesn't already have support for a "silent" flag, which, if set, will not cause the message to appear?
Can you link me to a technical analysis about this?
It would be one of the few phones where the baseband/SIM couldn't make changes to the system.
I don't have a link for a technical analysis of this, but I shouldn't need one. It should be self-evident that updating the OS is a process that is very obvious to the user. It's also something that Apple has never done without explicit action by the user to perform such an update. It would in fact be incredibly dangerous to update the OS without explicit action, if for no other reason than the fact that this would not give the user the chance to back up their phone in case something goes wrong.
I don't think Apple would want that capability either, but just for argument's sake.