The number isn't the issue here. Oliver killed a bunch of bad billionaires and their bad cronies and feels kinda bad about it, Malcolm murdered 500 innocent civilians and shows pretty much no remorse (maybe a tiny bit for his son, but even that seems pretty faint). At least in Sara's case she actually hurt innocents as an assassin, but she was so eaten up about it that she actually tried to kill herself to escape the life.
The reason no one is cutting Malcolm any slack is that he killed a huge number of innocents, seems not to care, and continues to murder and manipulate anyone (including his own children) so long as it protects him.
On the Flashpoint note, I'd love to see an alternate Arrow universe for an episode. (I need not to think about it too much, though, in case my brain starts to hope for things that won't ever happen, like a continuity change that brings Sara or Tommy or Shado back)