Islam acknowledges that force can (also) be used for good.
As for the burnt Quran copies, Qur'an has different readings, and the Arabic writing was not standardized at first. The books that were burned are Mushafs (Qur'an books) that were written in a different way than the standard.
Still, the main way Qur'an was preserved is via Oral Tradition, and there are multiple ways it could be read, but (as far as I know,) they're not contradictory, and complement each other, both in sound and meaning.
Here's one video I liked about different "Readings" of the Qur'an: