Malefic is less skeptical of Savage's genocidal plans than the rest of the Legion. After all, he's done it before.
Batman saying the Justice League is the plan against him seems a bit odd at first, but considering everything. If Batman ever became dark, he knows the League would be the first to realize how dangerous he is and would treat him like any Badass Normal baddie. Furthermore, it's why the League was founded. To ensure the safety of people. It's still somewhat dark to think about as seen below.
When Wonder Woman tore off Cyborg's arm, SHE STILL THOUGHT HE WAS CHEETAH! There is a reason you don't see what she sees when she does that.
More so the fact that she was willing to do it, despite the fact that Cheetah and Wonder Woman's rivalry is rarely given much explanation or backstory.
Though she did apologize after she tore it off and offered to help "her" get medical aid.
This also begs the question of how many average humans (civilians and cops) were just pummeled half to death by a crazed superheroine. Their limbs aren't quite as replaceable.
At the end of the movie, Superman points out that Batman never made a plan for if he himself went rogue. Batman replies that the Justice League is his failsafe. However, as the movie demonstrated, Batman was able to come up with very successful plans to defeat each of the Justice League, with only some slight modification to make them lethal. If Batman ever does go rogue, he's more than capable of handling the Justice League by himself! Especially since Superman gave him the kryptonite bullet.
This, in turn, implies that Batman expects that if he goes rogue, the League will kill him from a distance, before he's even capable of putting any of his plans in action.
DC Universe Online offers some voice clips of Batman explaining some of the contingency plans, as seen here.Batman's contingency plans involves distracting him using either his parents, or taking friends and family of Batman hostage.