At the end of the day, the NFL is trying to balance fair play with injury avoidance. The idea is that a QB shouldn't be allowed to avoid a sack by just flicking the ball away at the last moment. That's not fair to the defense who is about to sack the QB. The penalty for intentional grounding pretty much mimics what would have happened had the sack occurred instead.
A QB who is not under pressure who throws the ball away isn't avoiding anything. It's akin to any other player (or even the QB) just taking a knee at the line of scrimmage. So why would that player need to be penalized? No fair play issue here.
That said, they also put in the "outside of the tackle" rule. I think that exception is in place to 1) encourage QBs to scramble away from sacks and not just take them / get injured, 2) when a QB does scramble he is often subject to a potential wicked hit from a 270+ pound defender coming at him from the side at full steam, so this is to avoid a real major injury situation.