"Mahor yimharenah — to himself as a wife" — the Mekhilta reads this phrase as a limitation: the seducer may take the woman "as a wife that is permitted to him." This means the marriage must be halakhically valid. If Jewish law prohibits the match, the marriage cannot proceed — though the financial penalty still applies.
The Mekhilta lists the prohibited combinations. A widow may not marry a high priest. A divorcee or chalutzah (a woman who underwent the ceremony dissolving a levirate marriage) may not marry a regular priest. A mamzeret (a woman born from certain forbidden unions) and a Nathinah (a descendant of the Gibeonites) may not marry an Israelite. And the daughter of an Israelite may not marry a Nathin or a mamzer.
In all these cases, the seducer pays the financial penalty but cannot marry the woman. The knass and the marriage are separable. The Torah requires the payment regardless of whether the marriage can actually take place. The father collects the fifty shekels even when the law prohibits his daughter from becoming the seducer's wife.
This distinction between the financial obligation and the marriage obligation is important. The knass compensates the father for the diminishment of his daughter's marriageability. That diminishment occurred regardless of whether this particular seducer can legally marry her. The payment addresses the damage done, not the relationship that might follow.