It's no big deal. If you can save the root when you up-pot, fine. If you end up cutting it off, there's a very high probability it will do just fine anyway.
The only way a root will continue to grow after it has poked through a hole in this type of situation is if there is standing water or soil below, or if the environment is extremely humid. So if you don't want this to happen don't let it sit in water. If you are using bottom watering and having the water wick up, then it is inevitable that some roots will find their way into the water and grow into it.