*Laughs* OK, I have to say that's actually a nice touch. I had the same thing happen to me with
the burning ship in the harbor.
I figured I'd get around to it later, but instead I missed out on that one. As my girlfriend (a child therapist) would say, that's Natural Consequences for you. I enjoy actually having that be part of the game, myself.
I actually delayed making a decision on this one for some time, thinking I'd find a way to save both only to see in a post on Reddit that you can't. Guess I'm glad I caught that minor spoiler there, anyhow.
Now, as to the issue of game completion, I expect you'll be able to catch up to that stone later on. Hopefully someone else will confirm that.