If it is indeed a rape then why did she carry on with pregnancy, also she could've sought help from MC who i am sure would kill that person whoever it may be.... and if it was indeed her father, Hiroko kept on living at her parents home during pregnancy..and he is too obvious of a suspect..
It is indeed too convoluted theory and if its true then i would be happy however, IF MC did it then there would be no reason for Hiroko to keep it a secret since their relationship was on the verge of breaking up over this and knowing MC he would be happy to know that he is the father of Mao after all these years...and in addition to that Hiroko already knows about MC losing control which he says so himself when talking with Crazy nurse. And also Hiroko gets pregnant
before her first time with MC and says it was a one time thing...so its unlikely that MC impregnated her before their first time and lost memory over it (which hasn't happened so far except when he was drugged by Crazy)......And after all those years when they finally told the truth to Mao and she rebels, Hiroko could've easily told Mao if MC was the real father and avoided it....So taking all these into account its highly unlikely that MC could be the culprit....
However as u said since its a Harem focused game with ALPHA MC, it is hard to believe Hiroko cheated on him

Well i am more curious about the Why? than the Who?...which Blue will reveal the answer soon(er)?....