If an Orthodox rabbi tells you that a restaurant is kosher, and you see them serving something that is obviously treif, would you eat in the restaurant? Of course not! And you’d be over an issur if you did! (You would also probably call the rabbi and let him know what you saw.) The same is true regarding Shabat. We rely on rabbis when the halachah is unclear (sometimes even to poskim); we don’t need to ask shilahs on things that are obvious.
BTW my wife is a physician and was permitted to drive to the hospital on Shabat to take care of the patients.
Regarding the seemingly unfair penalties, the author of the Tosafot Yom Tov said that the reason that Jews were murdered in the Chmielnicki massacres was that we talked in shul.