Half orcs are pretty obviously derived from the man-orcs of Saruman.
I've always considered them to be a manufactured race which breeds true (after all, in a world where owlbears and halfdragon-anythings is possible, creating a race which was halfway between man and orc seems trivial).
Eberron had an interesting take on the issue, where the shadow marches had a population of men and orcs who get along just fine and sometime decide to make babies together because of love (just like with half-elves). This is another fine way to handle the situation.
Indeed, the whole idea of rape being behind a whole race seems the most ridiculous concept imaginable, as far as I'm concerned.