Yup the smell you are experiencing is most likely the result of organic life that was on the rock and is dying off. This releases ammonia and yes your tank will stink for a bit. It will pass once the denitrifying bacteria gets to work on it all and breaks it down into nitrates. As Neon said, if you can see any dead stuff in the tank or on the rocks, try removing it by hand, as this will speed the process up, since you are reducing the amount of material that can decay in the tank.
To expand on what Lynden suggested, you could also try using some filter wool. Cut a strip the width of your tank (back to front) and start at one end of the tank. Drag it half submergered and half out the water to the other end of the tank. A strip 3"-4" should be fine. All the gunk will be pushed up to one end of the tank and collect on the filter wool. The slower you do this, the better.