Flame,
I had the same problem and finally got it resolved. I had a guy come with a backhoe and fill in the trench (about half way) with dirt so that it was not so low. I then had him put in some large (8-10 inch) rock to slow down the water. Guess what the next heavy rain came and washed half the rock into my pond. Running water can do amazing things. I moved them back up to the drain and bought a lot of bag of concrete and spread it out over the rock and lightly watered it in. That did the trick. I guess what I an trying to tell you is that if you put in any small rock or small limestone it could go directly into your pond with the next rain. I would definitely look at large rock vs smaller rocks, then that may not be enough to slow down the water.
Joe