The Mekhilta strengthens the father's authority over a rapist's marriage through an a fortiori argument. With a seduced woman — where the seducer did not violate the father's will, since the daughter consented — the father may still abrogate or sustain the marriage as he chooses. He has full discretion.
With a raped woman — where the rapist violated both the woman's will and the father's will — the father's authority should be even stronger. If paternal consent is required when the act was consensual, how much more so when the act was violent and non-consensual!
The logic is compelling. The seducer acted with the woman's cooperation, yet the father can still block the marriage. The rapist acted against everyone's wishes, so the father should certainly have the power to refuse. The more egregious the crime, the stronger the father's veto.
This a fortiori argument closes any possible loophole in the law. Even if someone tried to argue that the rapist's marriage obligation in Deuteronomy is absolute and cannot be overridden, the Mekhilta's logical proof demonstrates otherwise. The father's authority scales with the severity of the offense. A crime that violated more people's autonomy cannot result in less parental control over the outcome. The rapist pays his penalty, but whether he marries is entirely the father's decision.