That's all part of the reason marriage was invented.
The marriage license is the man's legal permission to have sex with the woman.
Absent a marriage license between the man and woman, the default outcome is if the woman said she was raped, then she was raped (although in other cultures, it may be that if the man says the woman wanted it, then she wanted it).
In return, through marriage the man legally assumes responsibility for the woman and any offspring.
No different from driving a car: if someone says you stole the car you're driving from him, and you don't have proof he sold it to you, then you're a thief.