Statement 1:
"Fr. Martin is preaching tolerance toward people who have been hurt by the Catholic Church because of its dogma."

Statement 2:
"I don't see how this is different from the Catholic Church engaging in ecumenical dialogue."

You don't see the contradiction, do you?

Fr. Martin is a priest.  It is antithetical for him in that role to "engage in ecumenical dialogue" by taking a position so contrary to the teachings own his own Church, a position which says gays "have been hurt by the Church because of its dogma."