The difference, in my mind, is that it's literally Joe Kelly's job to hurl baseballs in the general direction of human beings, and that the hitter assumes this risk every time they step into the batter's box - which is why the pitcher always has some element of plausible deniability ("It just got away from me") when these things happen. If Kelly was deliberately headhunting, I might agree with you, but to me, a plunking on the back falls squarely within the category of things that may happen at a baseball game, intentionally or not.
But charging the mound and throwing punches at people? Always 100% intentional and within the batter's control, and IMO, whatever happens after that point is on you. Austin incited the entire incident and behaved like a punk from beginning to end, from getting up in Holt's face when he questioned the slide (if it was such an innocent play, why not a simple "My bad, bro. You okay?" and everyone moves on) to sucker-punching Febles during the brawl, and probably deserved a harsher penalty than what he got. Normally I find all of this business of retaliation and counter-retaliation pretty stupid, but I have a hard time finding fault with what the Red Sox did here.