You look at it this way.
Flagrant fouls are generally called when it is a malicious foul, or more than what was necessary to stop the play was done.
I highly doubt Rondo was intending to hurt Brad Miller in any way. He was trying to stop a lay-up that would tie the game.
When a pitcher deliberately throws the ball near someones head, he is out of the game. However, he could throw the same exact pitch by accident and stay in the game.
This is how the Flagrant call is intended to be called, malicious intent is one thing, trying to save or win a game is completely different.
In the end, if the refs botched the call it was certainly not a flagrant foul, if anything it was an intentional foul.
If anyone is going to say Rondo was stupid enough to commit a hard foul with 2 seconds on the clock they are just dumb.
The refs botched a lot of calls this game, particularly 3 of Ray Allen's 6 fouls. Ben Gordon jumps into his defender every time he shoots not giving the defended his rightful space.
There is so much to argue about in the officiating. Bottom line is, if you are an official and it is the last play of the game.
You do everything you can to allow the players to determine the outcome of the game. That's what they did.
Brad Miller had the opportunity to tie the game and he did not. Too bad.