It is said HoME 10; Myths Transformed) that Morgoth was filled with a nihilistic rage against all creation not of him and all living creatures in the world not of him [a.k.a every life sice only Eru could give that] and he would kill all and destroy all if he would gained the full control of Arda. Including Elves, Men, Orcs, trolls, animals etc etc
Sauron on the other hand did 'just' wanted to dominate all and rule as a god-king, in Myths Transformed it's directly stated he had not his former master's nihilistic side.
Not sure what part you are thinking of FC, but guess that ought to do with the fact that Sauron is not the forgiving type, any opposition he gladly retaliate upon.
Sauron would not kill off Men who obey him, he want to rule over them (PJ's films always added a to me pure dumb black & white-level on this, with all talk about the end for Men; Saruman in FotR the book even try to lure Gandalf to help him take control of the new Age of Men).
Actually if Morgoth even would killed everyone is unsure, I do not think so, as in other place in MT it's said that he during his reign came to like to be Lord over others as well as comments elsewhere that he wanted subjects.