The "super-pill" is an atrocious piece of Deux et Machina, literally. It makes Alfred strong enough knock-out Superman, but Batwoman can still have her neck snapped by Wonder Woman. Don't forget how Harley Quinn was able to waylay Lobo thanks to it. It's utter nonsense.
As for tackling "it" in Year Three, I believe they extended the question more than addressed it. It Wonder Woman could kill Huntress, then surely Superman, with his strength, durability and speed, could have done the same for the Batman.
It's an enjoyable farce, it you don't apply to much pressure to it, just like most video games are.
Well - in the series' defense, there have been multiple times when Superman could have stopped/killed Batman - and vice versa - but in each case, the would-be killer stopped because they remember the dynamic they used to have, and how good it was for the world. Each of them wants things to go back to the way it used to be, but Superman won't compromise on his regime ideas. So they are at a moralistic standstill.