I’ve been told by two competent rabbis that yes, but I just wanted to gain clarity on this again (to see why people believe that one can’t marry a Kohen in this case). Can a Jewish woman who has been raped by a Jew marry a Kohen? As mentioned, I’ve been told twice that yes. I wonder why people believe that no?

ב"ה Shalom, As Rabbi Elchanan Lewis clearly answered, according to the Shulchan Aruch Even Haezer 6; 8, and I should add also the Rambam (Issurei Biaah18:2 ) " if a woman has sexual relations with a man who she is Halachically prohibited to marry; she becomes a Zonah and can't marry a Cohen." This of course, does not mean, G-d forbid, that if the woman in not Halachically considered a "Zonah" she may carry on with promiscuous behavior because she will not be forbidden to a Cohen. On the other hand, laypeople who aren’t familiar with the details of Halacha, remember clearly the verse in the Torah Vayikra 21:7 that a Cohen may not marry a a Zonah= prostitute or a divorced woman and therefore think that a woman who was violated comes under the category of "zonah". However, a Rabbi who performs marriages must be fully fluent with these laws. All the best