The OP specifically referred to minhagim that have a clear basis in Halacha, which are the vast majority of minhagim. Of course, such minhagim should continue to be followed irrespective of what is stated in Mishna Berura. If I am not mistaken there is a story with the Chofetz Chaim himself who did something contrary to what he wrote in MB, and when asked he said that that he was doing as his father did.
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