I think you can safely remove the copper using EDTA. As Randy pointed out it also important to remove the EDTA, which is why I suggested soaking in water for another week following the initial EDTA treatment. To help remove any EDTA you could also soak in some mild acid overnight as this would help remove any EDTA bound to the rock. I think this would be safe and effective. There are also biodegradable chelating agents you can use such as nitrilotriacetic acid (NTA), ethylenediaminedisuccinic acid (EDDS), and iminodisuccinic acid (IDS). I have attached a review on these if you're interested. I would soak the rock in these compounds for 3 days (maybe repeat once for another 3 days with fresh compound), then in water for a week or two. Any residual chelating agents left in the rock will degrade in a few weeks, so you won't have any contamination.