Ouch.
No, coral sand and marine rock can indeed raise the ph and such, and the more you greater the change. Most rocks and sand are fine for fish tanks, but not all. But your tank is also in the middle of a cycle - did they test for ammonia as well? If not, I'm not convinced that the rocks caused the problem.
Ok. First off here is what I would do for your fish.
Empty the tank and refill it. Run it for 12 hours with the filter and all, and then you can introduce the fish back into the tank. You do not need your tank set up for 2 weeks empty - it's pointless. This is just in case you can't get them into someone elses tank.
There are a lot of people confused about the very start of setting up a fish tank. There are two stages to making the tank safe for fish. The first involves letting it sit empty, but running. This aerates the water and makes it safe for fish and takes no more than 12 hours on a properly filtered tank. Having the tank sit longer then this (or we can say 24 hours just to be safe) does nothing at all. No reason whatsoever to have a tank sitting empty for 2 weeks!
The second stage is the actual cycle, and this doesn't start until a source of ammonia is added to the tank, like fish. Fishless cycles come highly recommended, but since you already have the fish, that's not an option anyway.
So once it is aerated it is ready for fish. To avoid a second shock to the fish gradually, over a period of a couple of hours, add the proper water from the tank into the bucket with the messed up water, until it's about half/half. Then transfer the fish back.
Do a 25% water change the very next day, and you need to buy an ammonia tester and check regularly while your tank cycles, because any time it gets too high you will want to do a water change. If it's not too high, you should still do a water change every week.
Oh yeah, and chemicals. chemicals chemicals. Do yourself a favour and use nothing in the water except conditioner. Fish stores love to sell stuff. You don't need it. KISS, less will go wrong.
Not all marine rock is live folks.