By 1541 Luther was physically sick much of the time, spiritually-battle-scarred, and frankly just old and cranky. Most of the stuff Lutherans apologize for by Luther were written in the 1540s, the last years of Luther's life which ended in 1546. The "sides" were being drawn up by this time, not just between Catholic and Protestant, but already amidst Protestants, and lots of blood had already been spilled--usually in the name of punishing heretics.
In my opinion the 2nd generation of the Reformation--starting in the era of the Roman Counter-Reformation, was incredibly destructive to unity, in the name of orthodoxy, on all sides. The Church catholic has been desiring to get back to something like Regensburg for a long time....
Calvin, not Luther was the signal figure at Ratisborn, and if he found the statement acceptable, one must say that this made Charles V’s hopes for reconciliation vitually impossible. Recall that Luther had broken with Erasmus, and now we have a ferocious reasoner in Calvin, whose views were anithetical not only to those of Rome but of Constantinople. The East had not accepted Augustine and the West had softened his view; Now we have the arch-Augustinian, who for the last 25 years of his life dominated the Christian world.