Were they "justified"?? What kind of a question is that?
Federer obviously felt they were to act the way he did, noone else can judge that.
Were they "appropriate" for that moment? No, not really. The trophy ceremony is meant to be a celebration of the winner's success ASWELL AS the finalist (they receive a trophy too after all), and not a moment for the loser to wallow in self pity. Almost every other finalist ever has managed to compose themselves in that moment despite how horribly they must be feeling internally, and like it or lump it, it did mute the celebration of Rafa's victory, you could see it in Rafa's face, you can read it on this forum, you can witness it in the news reports today....
But such is sport, it's a volatile, emotional human pursuit and these things happen, Federer obviously couldn't help the tears, and at the end of the day Rafa still won and Federer still lost, so I don't let myself get too hung up about it