In the event a Kohen’s wife was R"L raped and he has to divorce her. In light of the difficult situation can he take her back as a pileagesh as he is not transgressing Lo Yikach as he in not marrying her?

לז"נ יונה שלמה בן ר' אברהם יוסף ז"ל ב"ה Shalom I first just wish to say that I am regarding your question as a theoretical one. The reason behind prohibiting a Kohen's wife according to the Gemara in Yevamot 56b, is either because of tum'ah or because she is considered a "zonah" ,since adultery was committed even though it was against her will. The status of a pilegesh, is one in which marital relations are permitted to one person, but the relationship between the man and the pilegesh is without a Ketuba. (See Sanhedrin 21a, Ra'avad on Rambam Hilchot Ishut 1:4) This being the case, taking the wife back as a pilegesh is not a solution. All the best. Happy Purim