Do male cats kill male kittens to get rid of competition? I heard that happens in the wild, but not sure if it is just an urban legend or not. Not sure what that is all about.
If mama kitty attacked him then he's not the father. Male cats will sometimes kill all the kittens (not just the males) so the prospective mate isn't wasting energy on offspring that isn't his. Lions do this, too. It's not unlikely that he's already gotten one or two. The behavior mostly shows up in barnyard or feral cats.