1. KS redirects the damage that should be done to the target, to the shooter. By redirecting sufficient amount of damage, effectively the shooter kills himself. The 'punishment' is straight forward in dealing out the following 'recommendations' to the players;
1) If you shoot at a friendly, you're gonna die, so don't do it.
2) If you run into a friendly fire wrecklessly, you're gonna get some else killed, so don't do it.
Your suggestion is much weaker in dealing out 1) and 2).
2. If you consciously aim and shoot at a friendly, or deliver sufficient amount of rounds, it will kill you instantly. KS is harsh.
However, KS is also thankfully lenient in some 'accidental cases'. Minor accidents really do happen, and with KS, an accidental round or two landed on a friendly is not gonna direct a fatal damage(unless it's something like a 40mm or 30mm). It might very lightly damage, or not damage at all - which would be sufficient reminder for the shooter to watch where he is firing.
If ammo was taken away the moment a bullet strikes a friendly, the consequences people have to deal with in making very small, minor mistakes would be all too harsh.
Besides, it'd make it even easier for stunninghunks to annoy someone on purpose. I've had a few cases of meeting KS offenders in H2H. They'd suddenly jump in front of you to annoy you on purpose. In many cases, my few shots landed on them, but I was able to stop fire at the right moment so I didn't suffer any more damage. Your suggestion of taking away ammo is gonna be extremely more easier to exploit.