Eating the substrate is certainly a risk as turtles are notoriously messy eaters. Though really, a lot of reptiles are in my experience. Since the substrate cannot be digested, it has the risk of causing impaction. Impaction is where the intestines are blocked by a foreign object, and nothing can be digested anymore.
The best way to avoid it is to use a separate container for feeding. One without substrate. It doesn't have to be a whole new tank just for feeding, it could be a moderate sized plastic bin. As long as it holds enough water to hold the turtle and let it move around a bit to gather the food.
While it might seem like a bit more work at first, it is actually easier to handle, as you can simply empty out the food tank and rinse it out. If you feed the turtle in the tank it lives in, you're going to have to take extra care to clean all the missed food out of the substrate. A gravel vacuum would help with that.
The only other option I really know of is to feed the turtle slowly, so that it catches all the food before it hits the gravel. It's not foolproof, and it's more time consuming than using a separate container for feeding I think.
