All I can say is this.. Celestia rules over an entire nation, If not continent. There will often be times she has to make choices she doesn't agree with. Be it for the benefit of the country as a whole, or those she watches over. Yes she has made mistakes. In banishing Nightmare Moon she prevented the entire planet from being plunged into a state where, plants would be unable to grow, season unable to change even with the weather ponies influence. Yes it cost her greatly in that she lost her sister to the moon for 1000 years.
Let me also ask you this. If the events were to continue while Twilight was under the effects of that potion, how do you know Celestia wouldn't have faced consequences for allowing her sister to become what she did and thus become a threat to Equestria? The issues surrounding Sunset Shimmer's banishment to another world. For all you know there could have been much more to it than what little exposition she provided Twilight. Perhaps she only told her what she needed to know so as not to be caught unawares by Sunset and left out details that would have made Twilight too afraid to go after the crown. Perhaps she exiled her to that world in hopes that being stripped of her magic would give her a new outlook on life and a fresh start at trying to become the type of pony Celestia had hoped she would become?
Am I dismissing the mistakes Celestia has made? No I know she made mistakes, many of them. But in a 22-24 minute show they can't show every consequence of each action taken by any particular cast member without straying from the message of that show. Besides it's a show that was originally designed for little children. Do you honestly think they would show such adult theme's like court hearings, punishment debates, etc. in a childrens show?