Obviously it was. The prayer book was oh so more important for posterity than the collected works of one of the greatest mechanical geniuses to ever to walk the Earth.
"Obviously it was."
There's nothing obvious about it. We have no way of knowing what the motivation of the recycler was, or how many duplicate copies he had.
Besides, from the little description we get from this article, it doesn't appear that there was anything there that the Church would have had any interest in suppressing, anyway.
Sounds like what Kansas wants to do to the very definition of science. Human nature never changes.
My guess is that the culprit was a math moron and couldn't have known the value of the text.
To be fair, during the period the manuscript was recycled, there was little interest in preserving classic texts other than within religious orders. During the renaissance, when people like Petrarch began to acquire and translate ancient works, the most common place to find them was in churches and monasteries.
Little merit or concern for it's preservation may have been the result of another extant manuscript on hand. (Let's remember that this copy was copied from yet another copy). It is also plausible that had this been kept intact as a work of Archimedes, it would have been sold off to some minor historian and lost forever.