Matzav, Rav Aharon Feldman, the Rosh HaYeshiva of Ner Israel has apologized for calling Rabbi Dov Lipman a Rasha. He did so after receiving a letter of explanation from Rabbi Lipman explaining that he was L'Shem Shomayim and only had the welfare of his community at heart.
Although he still strongly disagrees and calls him a 'Shogeg' (inadvertent transgressor) and misguided, R' Feldman realizes that Rabbi Lipman is indeed L'Shem Shomayim. He also said that he never called him Amalek or Haman. That's true. But he did say that he was a Shana U'Pireish. I guess he didn't remember that he said that.
In any event I give credit to the Rosh HaYeshiva for his honesty, ability to admit making a mistake in judgement and apologizing for it immediately. There is nothing wrong with disagreement. Even strong disagreement. An audio recording of his apology is available at Matzav.