Just dispose of the stopper. The package usually comes with enough for a replacement. If you dont have more stoppers, simply use a cut piece of rubberband bent in half or a piece of the tubing that comes on rapala trebles. I wouldn't bend the eye of the hook though; I'd be afraid it may take away from the action or fail on a hook up.
Now, I'm not sure how you are putting your trailer hook on but I prefer to put the trailer on the main and the rubber stopper after so the hook is not fixed to the main. When it's fixed, by inserting the eye of the trailer into the rubber stopper, it takes away from the way the spinnerbait swims IMO.
Wish I had a pic here, it would make it alot easier to understand. I hope you get my point.