Not OP, but from what I know about the whole topic:
Not the church in its whole, but very likely the persons involved with the case and likely the pope knew.
In the way of, "technically he might be right, but those technical details are attacking the philosophy and very foundations of our church, which already is under heavy attack from all sides"
So you likeley have pure power motivation, but for "true believers" it was more, basically attacking the foundations of the one and only true church (this is what "catholic" actually means). So even if what Galilei said sounds true and logical, it cannot be true as it would question the truth of the believe, which is not to be questioned. Therefore the logic must be wrong.
All they wanted was a way to punish him and going so clearly against "common sense" and orthodoxy was perfect and they used that.
The sentencing clearly states that the earth revolving around the sun "is a proposition absurd and false in philosophy, and formerly heretical", and by that time, Copernicus's De revolutionibus orbium coelestium had already been placed on the Index of Prohibited Books.
Are you saying the church actually knew Galileo was right, and did this anyway?