Yup, the discipline rating should really affect how many of those unnecessary penalties a player takes.
And isn't this a problem in general with sliders and attributes in the NHL games.
You have attributes that's on a 0-100 scale, but yet it seems that on zero it's still giving the player a pro attribute not too far after guy that's on 100.
Just like you said, if you set a slap shot attribute to zero on a guy, that fella should hardly be able to hit the puck, nevermind the goal.
Likewise if you set the penalty slider to max, the ref should call penalties every time two players happens to softly nudge each other, or if you set the CPU Penalty sliders to max, the players should just jump over the board every shift doing the best Paul Bunyan impression they can.
I.e with sliders/attributes on max or minimum it should give you "unrealistic" and excessive results... but most sliders in this game at best gives vague differences on ice.