Of course minhag trumps halachah, as shown by the numerous examples here. We embarrass ourselves by trying to claim otherwise.
In fact minhag can even trump something that would under normal circumstances be such an aveira that it would put you beyond the pale of Rabbinic Judaism. Just look at all the shuls that recite “Machnise Rachamim” in Selichot in clear violation of the Rambam’s ikkar. (Either that, or most shuls are run by apkorsim, chas v’shalom.)