Dumbledore (who has used Transfiguration in combat and lived) gave Harry his father's rock the day after Quirrell publicly accused Harry of always thinking purely of killing and novel ways to do it. I don't know if D wanted to encourage H in this, or to provide an alternative to some more dangerous action. (Maybe D has considered the possibility that Q has some dark reason for wanting Harry to learn the Killing Curse?) But I feel very sure that he was thinking of the use H did in fact make of it, and we don't need to imagine another purpose.

If anything, Dumbledore would want to keep the Philosopher's Stone more directly under his control, eg hidden under the lampshade in his office.