1.It isn't that it makes sense, it is to make the game more balanced.
If you can stealthily walk up behind someone and stab them or pummel them or whatever, and they don't notice, than the silenced kill allows you to remain hidden.
However, running around knifing someone all day is not a good idea, since people can just shoot you down while you are chasing someone.
2. You have this ability also, it isn't necessarily overpowered if everyone can do it.
If someone is charging at you attempting to melee, you need to either prepare your own melee, hopefully getting it off before him, or run backwards willy nilly, maybe do some jumps and keep shooting.
Melee is not overpowered, its just that many haven't figured out how to counter it.
Note: If you didn't have time for a counter, they just did their melee correctly. Be alert and cautious of potential hiding spots.