What do you mean, "unlike the story flag button"? That is the primary mechanism used to move posts away from the frontpage when it upsets someone. This is not particularly controversial - I feel you might have misunderstood something.
The story was not flagged, even though you feel it shouldn't have fallen of the front page (moot now they're merged). A flagged story will disappear, but after that it's HN algos that decide what sits on the front page.