Techncially, the Halacha requires that he divorce his wife in such a case. If it occurred before marriage then he is allowed to marry her if the attacker was a Kosher Jew (i.e. not a Goy, Mamzer, etc.). Some Poskim try to find Heterim to allow the Kohein to stay with his wife, for example if there were no actual Kosher Eidim. It does happen that a Kohein, unfortunately, has to divorce his wife in some cases like this.
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