I don't have the MMII yet, so I won't be too much help, but I'll list off what I can.
In 1E, the "malebranche" were listed among the various devils. Later, in 2E, they changed anything that had a bearing on real-world theology to different nomenclature to avoid pissing off the religiously intolerant. "Demons" became "tanar'ri", "devils" became "baatezu" etc.
I don't know why "malebranche" became "cornugon" but it may have had something to do with Nicolas Malebranche, a religious philosopher in the late 17th/early 18th century who was one of the principal figures in the development of Cartesianism. It doesn't make sense to me either, but I see no other reason for the name-change.
Later in 2E, we saw a return to the roots of planar things and creatures, such as tanar'ri again being called "demons", etc. There probably are a few places in 2E where cornugons are called malebranche again, though only in passing (try checking
Faces of Evil: the Fiends).
As for why they've made them two separate creatures in 3E...I have no idea.