You're right, of course.
There's an obvious problem in political theory called the Tyranny of the Majority. In modern times, this has gotten us Gorsuch. We can argue over the political merits of a heavily-conservative judge and gain no ground (and Gorsuch's most-famous action to date was to ignore a statement in a law claiming the law didn't apply to a thing, and apply it to that thing, so the problem of ignoring the rules because the rules let you do so is pervasive); yet one thing is clear: Gorsuch was elected by a simple majority due to the type of point of order tomfoolery described above.
The Tyranny of the Majority is guarded against by many things, and the best we had at the time was a Supermajority: three fifths must concur to prevent a momentary, slim grasp of power from making actions of long-term and extreme consequence. Turns out there's no such thing as a Supermajority if your Majority can just force the rule out. This must be a problem faced by all parliamentary organizations.
In a voting theory sense, we have other protections. Proportional representation for multi-seat elections (single transferable vote), and Smith-set single-seat elections (Ranked Pairs). The Smith Set is interesting: it's the smallest set of candidates who each would win in a one-on-one election with any candidate not in the Smith Set. When the Smith Set is one candidate, it's the Condorcet candidate, and represents the candidate by whom all are best served.
In a Yea or Nay vote, however, you have no protection. You can't change the voting method to protect against the simple majority. If the simple majority can violate any parliamentary rule, you have no protection against anything.