No one is saying that house arrest was the wrong move for the administrators who sentenced him to make. The problem is with the way you frame Galileo's house arrest (again, in the papal apartments, which by the standards of the day, when witches were being burned in Northern Europe, was mild). You are still working from within a paradigm characterized by the false dichotomy of Science vs. the Church, or enlightened Science vs. the Church as tyrannical, monolithic overlord. To say Galileo was persecuted for his ideas is saying too much; what do we make of those who actually were and are persecuted? Galileo had been announcing his ideas and squabbling with opponents for decades before it came to house arrest, with at least two discernible periods of conflict. The motive was by and large more personal than theological (and certainly not scientific). Even the idea that theological disagreement would land you on the pyre is flatly wrong. A counterexample of that is Aquinas whose ideas were condemned by the bishop of Paris. Aquinas was canonized 50 years after his death and declared a doctor of the Church two centuries later. He remains one of the most important thinkers of the Church, in philosophy and in history.

The strategy of casting oneself as a victim is a tried and tested method of gaining a politically useful yet illusory moral high ground with which to bludgeon your opponent, and the Church has no shortage of enemies.