The Marlins were upset at Morgan the night before plowing over the catcher (a play in which, had he slid, he probably would have been safe), dislocating his shoulder. So they hit him with a pitch.
Baseball is filled with unwritten rules and traditions, one of which is not to steal bases when the outcome of the game is no longer in doubt. When Morgan stole the two bases, the Nationals were down by 10 or more, and that violated the unwritten rule.
You may remember earlier in the year that a pitcher for the A's threw a fit when A-Rod crossed the mound when returning to first after running on a foul. It's another one of the unwritten rules, according to the pitcher.