Pulling off Fatalities on Captain Marvel in Mortal KombatVs.DC Universe becomes a whole lot more disturbing once you remember that Captain Marvel's secret identity is 10 year old Billy Batson. And Captain Marvel hanging around heroine like Princess Diana and the seductress Catwoman. Not very good for the child's psyche, I imagine.
Maybe in the DCU that crosses over with MK, Billy isn't a 10 year old kid.
When you perform a fatality on Green Lantern, how come his ring doesn't fly off in search of a new host?
Then, why is Green Lantern is not actively using his ring for Absolute Defense? Its because the Kombat Rage is a shade of Yellow, a colour to which the Ring of Will is weak against.
As for Superman being able to be hurt by normal bullets shot by Jax and Deathstroke? The wild kombat magic coursing through both universe. And putting up a Wild Mass Guessing here, probably the Kombat Rage magic have traces of harmful solar radiation that effect Superman.
In general, the separation of a Heroic Brutality from a Fatality is little more than what's said at the end of the fight.
Green Lantern's "Orb Squeeze" Heroic Brutality, involves him encasing his enemy in an orb, then levitating it, and crushing his enemy by shrinking the orb, a la Sonya Blade in Mortal Kombat 3. Where's the problem? It's NOT supposed to be lethal, however, during most other Heroic Brutalities, the loser wiggles around on the ground alot to prove they're not dead. But after this one the loser is eerily still...
Other examples are Superman and Sub-Zero's finishing moves. In Sub-Zero's case, he is nothing more than a man with ice powers yet his fatality is to deep freeze his enemy then shatter their body with a simple kick. In Superman's case, he freezes them with his cryo-breath, flies up the frozen opponent, drops them to the ground from very high up, then drops on them with the full weight of his body. Now not only does their body not shatter when they hit the ground, but they're somehow still alive after Superman drills himself into their chest. All this is ignoring the fact that the Rage that's infecting the superheroes should be causing them to go against their better judgment anyway (Flash is willing to kill when the Rage overcomes him in the story). The only reason it's a "Heroic Brutality" is because DC just can't tolerate their heroes crossing the line.
It may be an indication of how much Sub-Zero and Superman are holding back. For Sub-Zero, his more masterful use of ice may allow him to dictate when an enemy is shattered into pieces while Superman may not want to break his enemy apart.