I agree that with 13 pitchers and 13 position players on the roster, it seems like we should run pitchers out to the mound, even in a blowout. There are guys in the pen getting 2-3 innings a week. And god knows some of them could use the practice.
As for guys getting hammered, it is pretty simple. Cowboy has talked about it quite a bit. If you have command of your different pitches, you can work the edges of the strike zone, in/out/up/down, and keep the hitter uncomfortable. If you lack command, you are either walking guys, or leaving pitches right over the middle, which MLB hitters will hit hard, even if it is 95+ mph.
Why is Miley having success, even at 88-90 mph? He is throwing all of his various pitches on the edges of the strike zone and really mixing it up, keeping the batters off balance.