He should be fired for how badly he botched the play from the previous night. He stopped a live play because he realized he'd made the wrong call and then compounded it by arbitrarily deciding where everyone should be. He could have at least let it play out and then used replay to sort out his mess, but that was impossible after he turned an incorrect call into a judgment play.
However, everything about that benefitted the Royals and left the Indians with no recourse. Fortunately, KC blew the rally and Hernandez's double mistake didn't affect the score, but Kansas City had no excuse to be upset with him then or the next night.
The three ejections were completely justified (at least I'm assuming Matheny used some "magic words", Eldred and Singer were completely out of control). Was Ramirez hit by the pitch? I don't know, but it was an understandable call and it was upheld by replay. Accept it and move on. The balk that came a couple of at-bats later was blatant. It's often a difficult infraction to see, but that wasn't the case. I saw it live and the Indians broadcast team called it out before Hernandez did. The way the Royals reacted was completely out of line, but as others have pointed out, Hernandez has made himself a lightning rod and is a constant distraction even when he does thing correctly.