It should be fine, though depending on the airflow in your case, you may suck dust in through this new hole (not really a problem if you don't have dust filters anywhere else, and most don't).
You can cover it with some electrical tape if you really want, or try to find a bracket to cover the hole. They might have extras at a local computer repair shop, or if you have a friend who goes through lots of computer cases. If you really want, you can buy some, but that kind of cost seems unnecessary for something that most do-it-yourselfers have lying around.
By bracket I mean something like this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16811996009