I read that as "We already do this and it's frustrating, so why not do it for everything?" I know that's not what you meant, but that's what I think: not allowing +2 is frustrating and just makes it all that much easier to mess up. I feel like a DNF is a huge penalty because two of them in an average means you get pushed to the bottom of the ranking, kicking you out of any future rounds and preventing you from placing anywhere near the top. It is not always possible to prevent misalignments, except by waiting after the solve and putting the cube down carefully, and that isn't something the fastest people should have to do. So basically if you get an early DNF then it's just luck whether you can get an average or not. I don't like that.
Also, there's the intuitive fairness argument. If you get a misalignment that isn't your fault, and are given a +2, that's acceptable: the judge says "you take a 2 second penalty because the cube is misaligned" and you go "eh, alright, I'll be more careful next time." So that's a fair penalty, because luck (or being super careful about putting the cube down) can affect a solve by more than 2 seconds by itself. But if you get a DNF, then it's more like this: the judge says "looks like it's above 45 degrees off, so the cube isn't solved, DNF" and you go "seriously? it wasn't my fault!" and then the judge replies "sorry, those are the rules." It ends up feeling way more unfair and frustrating.
EDIT: My approach in different terms: Suppose you have an unruly child and they break a $30 item while you aren't watching them. The +2 penalty is like the shopkeeper asking you to pay them $50 to compensate for the item and to make you be more careful in the future; that is a relatively reasonable request. The DNF penalty is like the shopkeeper breaking your leg.