If there was a minhag Yisrael (a minhag accepted by all of clal Yisrael) which had a good reason but was causing people to go off the Derech would that be grounds to abrogate/ignore the minhag? Would it be considered like Sakanat Nifashot/danger to life or rendered null due to some other mechanism? Or do we still keep the Minhag around?
THe answers are Yes and No, depends on some details you didn't provide:
Many of earlier Minhagim made their way into the firm Halachah and are not subjects to change anytime soon. E.g. the Gomorrah in Brachot (31a "דאמר ר' זירא: בנות ישראל החמירו על עצמן שאפילו רואות טיפת דם כחרדל- יושבת עליה שבעה נקיים") about women waiting for 7 clean days for every stain, which was a Minhag that turned to Halachah Psukah very fast and we currently can not turn it back in any way.
Many Minhagim that were instituted in medieval times, like numerous additions to the Teffilah, by Rishonim or Achronim require at least a Gdol Hador or two to offer an alternative solution, as we hold that only a court equal in wisdom can repeal decisions of an earlier court.
Some Minhagim (e.g. that are phrased by the Achronim as "יש אומרים" (some say) can surely be overridden by more important considerations, like future observing of Mitzvot, as the Gemmorah in Yoma 85b says:
"ר' שמעון בן מנסיא אומר ושמרו בני ישראל את השבת אמרה תורה חלל עליו שבת אחת כדי שישמור שבתות הרבה, א"ר יהודה אמר שמואל אי הואי התם הוא אמינא דידי עדיפא מדידהו וחי בהם ולא שימות בהם, אמר רבא לכולהו אית להו פירכא בר מדשמואל דלית ליה פירכא וכו' אשכחן ודאי ספק מנא לן ודשמואל ודאי לית ליה פירכא"
"Rabbi Shimon ben Menasya said: It is stated: “And the children of Israel shall keep Shabbat, to observe Shabbat” (Exodus 31:16).The Torah said: Desecrate one Shabbat on his behalf so he will observe many Shabbatot. Rav Yehuda said that Shmuel said: If I would have been there among those Sages who debated this question, I would have said that my proof is preferable to theirs, as it states: “You shall keep My statutes and My ordinances, which a person shall do and live by them” (Leviticus 18:5), and not that he should die by them. In all circumstances, one must take care not to die as a result of fulfilling the mitzvot."