I believe it does matter! It's the same thing as the difference between playing Halo 3 and dying to somebody who outmaneuvers you, takes you by surprise and uses superior skills to kill you with the Assault Rifle, or somebody who walks straight up to you and uses the Battle Rifle to kill you almost instantaneously. Both of these things end in death, but one of them feels a lot more frustrating to most players because of how inherently unfair it seems to have all of these weapons if only one of them is actually worth using. Compare that to LoL, where we have all of these mages with different attacks and spells and stuff, but why would you use any of them except the ones with instant/homing stuns?
Don't worry, I agree. I believe that game design still hasn't moved past the "here's a broken game, have fun" mentality, and I think that it's silly for anyone to imply that it can't. Tensei and Zero are right in that removing CC specifically from the structure of DotA wouldn't really work, but I believe all that means is that DotA itself is generally flawed. I'm not arguing that we should crack DotA in half or all stop playing it forever, but I do believe that trying to justify bad design elements will only continue to slow down game design, especially competitively.