As I understand it, if a Kohen is certain that his wife was violated by another man, their union is now prohibited and a divorce would be needed. A kohen is prohibited from being married to an isha zonah, which the Talmud defines as a woman who has had relations with any man -- regardless of her choice in the matter! -- other than her husband, with the exception of premarital relations with a Jew (which does not disqualify a woman from marrying a kohen). Thus if a married woman is raped, her rapist is "another man", and she can't go home to her kohen husband. (If the husband is not a kohen, the couple is prohibited from reuniting only if she chose to "betray" her husband, not if she was raped.)
Rabbi Aaron Rothkoff-Rakeffet tells of a tragic such case years ago in Philadelphia, if I recall correctly, where she was raped on the way to/from the mikvah, which was still located in the older, sketchier part of town; as her husband was a Kohen, a divorce was needed. May God have mercy.
I think there may be some discussion about what constitutes "certainty" on the husband's part, or if he could try to argue he doesn't believe it really happened or the like -- but that only goes so far.
Nagah quoted a fascinating responsum of Rabbi Moshe Feinstein (EH I:24):
Even if the wife was incredibly modest and had no business with other men and there was no conflict in their marriage, they were always peacefully in love -- perhaps she wanted to leave her husband and marry another man for whatever reason. Therefore [the husband's] saying that he believes [his wife was raped] is worthless; we must tell the husband "your belief is mistaken", he must put those thoughts aside.
You can tell me I've watched too much L&O:SVU, but it really bothers me to say "oh she was making up a rape allegation"; I really wonder how far you can take that. Let's say they're able to arrest and convict the rapist with strong evidence? Do we still say nothing happened?
There may be other halachic loopholes of which I'm unaware, but generally speaking yes, this is a really awful tragedy. (Also be aware that the halachic definition of violation here is quite specific; it's certainly possible she was sexually abused in a different way, which would get us out of this problem.)
Years ago there was a nominally-affiliated Jewish man who met a non-Jewish woman interested in spiritual growth; eventually they reached full observance, she was preparing for conversion to Judaism, and plans for marriage were made. Then it was discovered that he was a Kohen (note: the "duchening hands" picture on a tombstone may not establish sufficient proof of Kohen status, that may just have been "stock Hebrew icon #3A" from a catalog that someone selected). Rabbi Joseph Dov Soloveichik observed that there is no good way we can try to explain this; we simply say that when the rubber meets the road we are obligated to submit to the will of a G-d whose ways we don't always understand, and each of them will have to pick up the pieces of their lives and try to find someone else. (I've heard others try to say "explain to them about what a precious thing kehuna is to us; I guess if that floats your boat, fine.)
I don't think you can offer a better explanation here. We have a system of laws that we believe were given by G-d, and we abide by them without exception. Generally, doing so can lead to personal fulfilment and wellbeing, but ultimately it is not ourselves -- nor our sense of "fairness" -- that we worship. (Rabbi Soloveichik observed that Father Abraham was prepared to carry out the child sacrifice of his son, though that would have meant his life's mission of spreading ethical monotheism would have been seen as a failure -- because the will of G-d, not our own "personal fulfilment" -- is the be-all, end-all. This is a difficult message for a generation focused on "this is good for me.")
Tragic cases like this one prove that religion is about more than just ourselves; we pray never to be put to the test like that.