But that negativity you are referring to is an opinion- a quality specific to that particular moment.
To put it into perspective better to suit that the penalties are not in need of improvement, as the player commiting the action you would have to think on the situation. Since everyone loves talking of Durant, I'll continue-
IF the player opts not to take the prize, then the player is now aware that their opponent has full control of the game (at least to an extent) and is priveleged in knowing information revealed through the penalty (such that a card that may have been useful was the random one put back).
IF the player takes the penalty, the player now has to see that the game can change more than what was expected. That drawn card could be anything. It may hurt, it may help. But regardless, you won't find out until their next draw, where afterwards they could play the prize or the card they drew, and you'll never quite know which was which or if it was still in their hand. It's a large disadvantage in terms of you just don't know what is going to happen, but now there are more options, applicable or not.
For "better" players, they will be able to play around it, but that's irrelevant as not "Everyone" is better.
The situation you described is, if I understand the playstyle of Durant decks, actually quite common in such decks when it comes to penalties, isn't it? I believe it also is a general problem with penalties for Gengar-based decks, although I'll admit I know little of those.
Besides, the fact that sometimes the penalty will benefit the offending player no matter what is an argument for changing the penalty system, not against.