Quartz is safe, provided there is nothing toxic within it that might leech out. "Rust" on the surface could be iron for instance. There was a photo of this in another thread just last week.
Most "regular" type aquarium gravel is made from quartz and it is inert.
I would recommend just scrubbing the rock with a good heavy-duty brush under the hot water tap. This is hot enough to clean the surface, but not sufficient to crack the rock.
The "acid" test won't be necessary if it is true quartz, but if you're not sure, you could put a few drops of a strong acid and if it fizzes the rock is calcareous (and obviously not quartz). A good acid to use is the regent #1 of a nitrate test kit which contains acid. Common vinegar is often suggested, but it is not really a strong enough acid [we do eat it after all] to be certain.
Not that you're proposing to do this, but for the benefit of others reading--never boil rocks; they can explode. The "cracking" was as previously explained due to the temperature difference.