I think you're right that most of the officiating was fair. Fouls / free throws don't tell the whole story because of differences in styles of play. When the foul count at the start was 6-0 or something, w/a few on Stiemsma, that was about right, though lopsided.
That said, I think some of the no-calls / questionable calls were late in the game, were critical and went Miami's way. I don't think Pierce's 6th was a foul on him. That call, obviously, was huge since it put him out of the game. The call on Garnett when Wade also kicked him -- that can go either way, but I think the offensive player's leg out usually is a red flag these days for refs. Hitting Rondo on the head on his drive.