I think this episode of Fairy tail was probably one of the most touching as well as most epic :D I think the whole reason behind why Freed starts to cry is when Mirajane says, "When people realize how lonely it is being alone, they become kind. And, you`ve realized it..." Which brought out his feelings guilt for attacking his guild mates, and the feelings of loneliness he had been trying to surpress for so long. I think Mirajane had known Freed was lonely deep down, and once he realized she cared, thats what really brought the tears to his eyes :)