In my experience there really isn't much you can do - without getting a dog (and having the "fun" of introducing your cat to the dog) the best I've ever managed is to chase the offending cat off my property any time I see him around. That tends to make the tomcat a bit more circumspect around your property - which should give your cat a safe-ish outdoor area.
The only other option I can suggest is an outdoor cat run she can access from indoors (usually via a cat door) where she has plenty of space but the tomcat can't get to her. That's going to cost you either money or time.
Unfortunately, your cat being spayed isn't enough for some toms, particularly if there's a queen in heat and they can't get to her. They're going to try to mate with anything feline that holds still long enough.
Also, there's some dominance behavior going on here - the tom regards your property as part of his territory, and he's trying to ensure that your cat acknowledges him as the top cat.
I'd suggest you keep an eye on her - in situations like this it's not uncommon for the female cat to be injured trying to escape the tom. More than once I've had to take neutered females to the vet to treat bad claw wounds near the base of the tail.