In most US States (probably all of them) failure to follow the Lawful orders of a police officer is itself a crime, and is grounds for the officer to arrest the person, even if the person had not done anything wrong prior to that.
This obviously leads to the question: what orders are lawful? The officer has a pretty broad range of discretion. Ordering a person out of a car, or to roll down a car window, is pretty clearly lawful. Ordering a person to commit a crime would not be lawful. Neither would ordering a person to submit while the officer rapes or robs the individual be lawful.
In practice, the officer will usually think that all of his or her commands are lawful, and might feel threatened by any failure to comply. In which case, the officer might shoot. This might not be upheld later if the command was not lawful and/or the officer's fear was not reasonable, but that will do the person shot little good. It is usually wise to comply with any commend, unless it puts you very directly at serious risk.
Remember you don't know what else has happed to the officer that day. Has the officer had a fight with his/her spouse that morning? Just been denied a promotion? Been turned down for a mortgage? None of that should matter, legally, but it will affect the officer's attitude, and can lead to escalation, even if the person stopped is in no way at fault.
An instruction to "shut up" is probably not going to provoke an officer to shoot if it is disobeyed, but it might help to escalate the situation. It is probably lawful, depending non the exact circumstances. As to the first amendment issues, that would probably come under the 'time, place, or manner" regulations that may be applied to speech. And even if it is not held to be lawful, the time to contest it is in court, not during the stop.
If the officer feels safer with the window fully rolled down so that the officer could reach in, that is probably a lawful command.