a competitively balanced game is a balanced game. the weapons in this game are so completely out of wack and relying on the only way that the game is played seriously as the benchmark to balance the weapons on is by far the best way to balance.
bonk is broken for a number of reasons. the scout is at his highest damage potential when he is close to an unaware enemy. in order for a scout to do this, he has to navigate the map in a way that prevents him from taking fights against groups of enemies and find opportunities to attack people who are not suspecting a scout to be behind them. right now, it is painfully easy to pop bonk, run a mile behind the enemy team, and then take a fight in exactly the way the scout wants to take a fight, whether harassing enemies as they spawn or finding enemies that are behind the main line of fighting and easily picking them off.
losing the pistol doesn't effect scout significantly for a number of reasons. first, scout has the most powerful close range weapon in the game, which encourages a scout to fight in that range. second, the scouts high move speed and double jump makes tracking as a scout player more difficult in close and mid range fights, making the scattergun more reliable in both of those situations. third, the pistols random spread beyond the first bullet means that the pistol is not reliable in any sense of the word beyond mid-range, where the scattergun is already a superior weapon. fourth, even if you are out of scattergun shots and reloading one at a time, the scattergun's dps is still comparable (only slightly worse) than the pistol at mid range assuming you hit every shot.
so, look at the fact the bonk changes out your weak long-mid range weapon with an option to effortlessly get into close range with an enemy and it becomes pretty obvious why the bonk is not a well balanced weapon.