Discipline. While that is normal behavior for dogs, he may be big enough to actually hurt her. While she can handle roughhousing and playing, if he was to actually achieve intercourse with her when she's that young he could cause her great injury. Watch what they do and how she responds; if he's just play-humping her and not trying to have intercourse then that part won't be much of a concern. Pay attention to how she responds: if she reacts playfully then there isn't anything to worry about, but if she reacts with yelping in pain or collapsing under his weight then you need to intervene. You have to apply more discipline in firmly telling him "NO!" and getting him off of her. Separate them entirely if you have to, especially when nobody will be around to protect her. (And if they are only playing around but you just don't like seeing an action that resembles sex then shït, get over yourself.)
She's still small and growing yet. In a few months she will be bigger and more able to push back against his size. (I'm going to assume they're breeds of roughly the same size and not something like a mastiff and a chihuahua.) Also, his being "on guard" may be his instinct to protect his younger pack mate.
If you haven't already, take him in for a vasectomy. You don't have to do something as invasive and barbaric as having him fully castrated. A vasectomy will sterilize him so he can't impregnate her, and it will spare her the far more invasive surgery of being spayed. Plus, once they are both sexually mature, it will allow them to enjoy the pleasures of sex (again, assuming they are of compatible size) without resulting in a litter of puppies you likely wouldn't be prepared to take care of.