Killing lots of people also does an interesting thing in the game besides getting rid of your Karma:
A: Brings the wrath of the law. Cops and district attornies will view your character as a murderer, because he is. The Punisher in crime terms has committed about 2,500 to 3,000 murders...which is totally insane since the most hostile real-life serial killer has probably only killed in the 250 range (this is very open to debate but very hard to proove and probably not so good a topic for this board since there are kids on here). My point, Frank is a much more wanted man than any of the criminals he is hunting these days, even if 2/3rds of his body count is self defense, which is unlikely since he is hunting the villians. You mow down all the bad guys, you will be viewed as a bad guy.
B: Brings the wrath of players who have taken the code against killing. The Punisher is never going to be an Avenger (outside of a What If? comic). The fact that Captain America has not hunted him down is a lapse in the Marvel Universe continuety in my eyes, since Frank is a much more dangerious killer than a mysterious group of guys in the skull masks shouting "Justice is served!" and blasting minor super villians. Fool Killer is never going to team up with a bunch of civic minded hero people in Manhattan and take down the mob (although he did get his own limited edition), so if you "off" to many bad guys, you will be viewed as a bad guy and hunted down by the characters who see themselves as good guys.
My character has planted several villians over the years....as has Thor, Batman and even Captain America, sometimes it is part of the job BUT it is NOT the job...then you are just a psycho.
This doesn't mean he can't be the team loose cannon. Get all crazy and nearly go too far every once in a while.
Besides, if he kills the badguys off, how in the world will he be able to foster the burning, seething hatred that takes decades and makes great enemies?