There's something called PABS - Pet AntiBreeding System. It's basically a rear-end harness and diaper your female can wear to protect her. They are in all different sizes and a pad can be slipped in a provided slot for later use when she starts to go into heat to keep mess at a minimum.
I'm not sure what you plan for the future but once they are old enough/at sexual maturity (females usually start first heat at age of around 6 months, thus are able to get pregnant then). There are additional options including: spaying/neutering, and for those who are interested in surgery or may want to breed later down the road there's doggie birth control, prescribed by vets.
If the fear is just hurting her, try the PABS online or local pet store. The humping at his age is not unusual, so don't think you've done anything wrong or wonder if she's abnormal - totally normal at this age, the humping will continue if unfixed though.