No, I don't think Ortiz should have thrown the bats - a very dumb move. But, possibly the real culprit was Terry Francona - who did nothing all night long to protect his starter and his hitters as the home plate ump either missed strike calls when Pedro was on the mound or squeezed the hitters when the Sox were at the plate. It was obvious, and even Jerry Remy made a clear point of it.
However, it was the same ump who made questionable calls against the Angels as well - and you'll remember that Mike Scioscia came out of the dugout early in the game to make the ump aware that he was watching what was going on. Scioscia didn't get tossed because he didn't try to make the ump look bad, but his team saw what he did. And the Red Sox, with no visible defense from Francona, did what players do in that situation - stand up for themselves.
Ortiz was still wrong. But maybe he wouldn't have reached that frustration level if Francona had made his presence felt and stood up for Pedro and his team. Part of the manager's job, plain and simple.
And this "minor" point may cost the Sox the services of Ortiz for 5 or 10 games - and that is a problem.