Straight-up orcs would make more sense, but I like the idea of half-elves, especially if (fluff-wise) they can become a whole community to themselves, kinda like the Metis. The rape explanation is less likely with half-elves, and frankly I think it should be routed out regardless. I don't like that it's the go-to explanation.
That's the reason I don't like it, as well. My group has grown out of it, mercifully, but I still see it a lot in other players. Personally, I just don't like the idea that either kind of halfbreed is common enough and recognised enough to be a "core race". I like halfbreeds, but I like it when they're odd and unusual, like your ligers and wolf-dogs and "wholphins".
And it seems like they should result in a variety of different traits depending on their parents/genetics, not in a distinct race. I'd also like to know why it's so
very common to find humans interbred with orcs or elves, but not with any other humanoid races. The fact that the next most common would be celestials and infernals (aasimar, tieflings) would seem to pose a very odd genetic question.
If they're supposed to be a distinct race (breeding true) that
originally descended from halfbreeds, that's fine - that's what helfs and horcs are in
Races of Destiny, IIRC - but at least give them their own names, them.